[package - 123arm64-quarterly][biology/py-pysam] Failed for py39-pysam-0.19.1 in build
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Date: Sun, 10 Jul 2022 07:40:09 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: http://ampere1.nyi.freebsd.org/data/123arm64-quarterly/dd322eb69d47/logs/py39-pysam-0.19.1.log
Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=123arm64-quarterly&build=dd322eb69d47
Log:
=>> Building biology/py-pysam
build started at Sun Jul 10 07:34:29 UTC 2022
port directory: /usr/ports/biology/py-pysam
package name: py39-pysam-0.19.1
building for: FreeBSD 123arm64-quarterly-job-01 12.3-RELEASE-p5 FreeBSD 12.3-RELEASE-p5 arm64
maintained by: yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py39-pysam-0.19.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.3.pkg
[123arm64-quarterly-job-01] Installing pkg-1.18.3...
[123arm64-quarterly-job-01] Extracting pkg-1.18.3: .......... done
===> py39-pysam-0.19.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-pysam-0.19.1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py39-pysam-0.19.1 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py39-pysam-0.19.1 for building
=> SHA256 Checksum OK for pysam-0.19.1.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py39-pysam-0.19.1 for building
===> Extracting for py39-pysam-0.19.1
=> SHA256 Checksum OK for pysam-0.19.1.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py39-pysam-0.19.1
===> Applying FreeBSD patches for py39-pysam-0.19.1 from /usr/ports/biology/py-pysam/files
===========================================================================
=======================<phase: build-depends >============================
===> py39-pysam-0.19.1 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[123arm64-quarterly-job-01] Installing gmake-4.3_2...
[123arm64-quarterly-job-01] `-- Installing gettext-runtime-0.21...
[123arm64-quarterly-job-01] | `-- Installing indexinfo-0.3.1...
[123arm64-quarterly-job-01] | `-- Extracting indexinfo-0.3.1: .... done
[123arm64-quarterly-job-01] `-- Extracting gettext-runtime-0.21: .......... done
[123arm64-quarterly-job-01] Extracting gmake-4.3_2: .......... done
===> py39-pysam-0.19.1 depends on package: gmake>=4.3 - found
===> Returning to build of py39-pysam-0.19.1
===> py39-pysam-0.19.1 depends on executable: cython-3.9 - not found
===> Installing existing package /packages/All/py39-cython-0.29.30_1.pkg
[123arm64-quarterly-job-01] Installing py39-cython-0.29.30_1...
[123arm64-quarterly-job-01] `-- Installing py39-setuptools-62.1.0_1...
[123arm64-quarterly-job-01] | `-- Installing python39-3.9.13...
[123arm64-quarterly-job-01] | | `-- Installing libffi-3.4.2...
[123arm64-quarterly-job-01] | | `-- Extracting libffi-3.4.2: .......... done
[123arm64-quarterly-job-01] | | `-- Installing mpdecimal-2.5.1...
[123arm64-quarterly-job-01] | | `-- Extracting mpdecimal-2.5.1: .......... done
[123arm64-quarterly-job-01] | | `-- Installing readline-8.1.2...
[123arm64-quarterly-job-01] | | `-- Extracting readline-8.1.2: .......... done
<snip>
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/htscodecs/htscodecs/rANS_static4x16pr.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/rANS_static4x16pr.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/htscodecs/htscodecs/rle.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/rle.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/htscodecs/htscodecs/tokenise_name3.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/tokenise_name3.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/kfunc.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/kstring.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/md5.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/multipart.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/probaln.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/realn.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/regidx.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/region.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/region.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/sam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/synced_bcf_reader.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/tbx.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/textutils.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/thread_pool.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
htslib/thread_pool.c:699:9: warning: code will never be executed [-Wunreachable-code]
printf("%d waiting, %d running, %d output, %d, arun %d => %d\t", p->njobs,
^~~~~~
htslib/thread_pool.c:698:9: note: silence by adding parentheses to mark code as explicitly dead
if (0) {
^
/* DISABLES CODE */ ( )
1 warning generated.
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/vcf.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/vcf_sweep.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/vcfutils.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/htslib_util.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libchtslib.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/bcf_sr_sort.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/bgzf.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_codecs.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_decode.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_encode.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_external.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_index.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_io.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_stats.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/mFILE.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/open_trace_file.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/pooled_
alloc.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/string_alloc.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/errmod.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/faidx.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/header.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/hfile.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/hts.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/hts_expr.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/hts_os.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/arith_dynamic.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/fqzcomp_qual.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/htscodecs.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/pack.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/ht
scodecs/rANS_static.o build/temp.freebsd-12.!
3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/rANS_static4x16pr.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/rle.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/tokenise_name3.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/kfunc.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/kstring.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/md5.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/multipart.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/probaln.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/realn.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/regidx.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/region.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/sam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/synced_bcf_reader.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39
/htslib/tbx.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/textutils.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/thread_pool.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/vcf.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/vcf_sweep.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/vcfutils.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/htslib_util.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libchtslib.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libchtslib.cpython-39.s
o -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
building 'pysam.libcsamtools' extension
creating build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools
creating build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/lz4
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcsamtools.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/amplicon_stats.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam2depth.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_aux.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_cat.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_color.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_consensus.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_fastq.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_flags.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_import.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_index.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_mate.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_md.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_samples.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_sort.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_split.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_stat.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bamshuf.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bamtk.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bedcov.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bedidx.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/consensus_pileup.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/coverage.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/cut_target.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/dict.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/faidx.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/lz4/lz4.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/padding.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/phase.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/sam_opts.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/sam_utils.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/sam_view.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/sample.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/samtools.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/stats.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/stats_isize.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/tmp_file.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcsamtools.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/amplicon_stats.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam2depth.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_addrprg.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_ampliconclip.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_aux.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_cat.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_color.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_consensus.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_fastq.c.pysam.o build/temp.free
bsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_flags.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_import.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_index.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_lpileup.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_markdup.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_mate.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_md.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_plbuf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_plcmd.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_quickcheck.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_reheader.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_rmdup.c.pysam.o build/temp.freebsd-12.3-RELEASE
-p5-arm64-cpython-39/samtools/bam_rmdupse.c.!
pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_samples.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_sort.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_split.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_stat.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bamshuf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bamtk.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bedcov.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bedidx.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/consensus_pileup.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/coverage.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/cut_target.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/dict.c.pysam.o build/temp.freebsd-12.3-REL
EASE-p5-arm64-cpython-39/samtools/faidx.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/lz4/lz4.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/padding.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/phase.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sam_opts.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sam_utils.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sam_view.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sample.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/samtools.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/stats.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/stats_isize.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/tmp_file.c.pysam.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/p
orts/biology/py-pysam/work-py39/pysam-0.19.1!
/pysam -L!
/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcsamtools.cpython-39.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/HMM.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/abuf.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/bcftools.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/bin.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/ccall.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/cols.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/consensus.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/convert.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/convert.c.pysam.c:534:66: warning: code will never be executed [-Wunreachable-code]
default: error("Unexpected type: %d\n", fmt->fmt->type); bcftools_exit(1); break;
^~~~~~~~~~~~~
1 warning generated.
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/csq.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/dist.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/em.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/extsort.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/filter.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/filter.c.pysam.c:3422:12: warning: code will never be executed [-Wunreachable-code]
if (0) filter_debug_print(out, NULL, nout);
^~~~~~~~~~~~~~~~~~
bcftools/filter.c.pysam.c:3422:9: note: silence by adding parentheses to mark code as explicitly dead
if (0) filter_debug_print(out, NULL, nout);
^
/* DISABLES CODE */ ( )
1 warning generated.
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/gvcf.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/hclust.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/kmin.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/main.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/mcall.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/mpileup.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/ploidy.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/prob1.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/regidx.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/reheader.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/str_finder.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/tabix.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/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]
detect = 0;
^
1 warning generated.
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfgtcheck.c.pysam.c:1189:39: warning: code will never be executed [-Wunreachable-code]
args->min_inter_err = strtod(optarg,&tmp);
^~~~~~
1 warning generated.
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfhead.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfview.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcmp.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/version.c.pysam.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcbcftools.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/HMM.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/abuf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bam2bcf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bam2bcf_indel.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bam_sample.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bcftools.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bin.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/ccall.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/cols.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/consensus.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/convert.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cp
ython-39/bcftools/csq.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/dist.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/em.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/extsort.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/filter.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/gvcf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/hclust.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/kmin.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/main.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/mcall.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/mpileup.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/ploidy.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/prob1.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-
cpython-39/bcftools/regidx.c.pysam.o build/t!
emp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/reheader.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/smpl_ilist.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/str_finder.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/tabix.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/tsv2vcf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfannotate.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfbuf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfcall.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfcnv.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfconcat.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfconvert.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcffilter.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-c
python-39/bcftools/vcfgtcheck.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfhead.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfindex.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfisec.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfmerge.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfnorm.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfplugin.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfquery.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfroh.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfsom.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfsort.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfstats.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfview.c.pysam.o build
/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-!
39/bcftoo!
ls/vcmp.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/version.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcbcftools.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcbcftools.cpython-39.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcutils.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/pysam_util.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcutils.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/pysam_util.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcsamtools.cpython-39 -lcbcftools.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcutils.cpython-39.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcalignmentfile.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcalignmentfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcalignmentfile.cpython-39.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcsamfile.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcsamfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcsamfile.cpython-39.so -Wl,-
rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcalignedsegment.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcalignedsegment.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3
-RELEASE-p5-arm64-cpython-39/pysam/libcalignedsegment.cpython-39.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libctabix.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libctabix.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpytho
n-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libctabix.cpython-39.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcfaidx.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcfaidx.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam
-L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcfaidx.cpython-39.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcbcf.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcbcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -
Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcbcf.cpython-39.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcbgzf.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcbgzf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam
-Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcbgzf.cpython-39.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libctabixproxies.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libctabixproxies.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-3
9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libctabixproxies.cpython-39.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
cc -Wno-unused-result -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-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcvcf.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcvcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -
Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcvcf.cpython-39.so -Wl,-rpath,$ORIGIN
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.6
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.5
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.3
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.7
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.4
error: symbols defined in multiple extensions
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/py-pysam