Broken on aarch64 architecture: conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.9

[yurivict]

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-13.0-RELEASE-p11-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-13.0-RELEASE-p11-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-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython
 -39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-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.9
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.10
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.2
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.4
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.5
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.6
error: symbols defined in multiple extensions
*** Error code 1

It also breaks on the riscv64 architecture in a similar way:

/nxb-bin/usr/bin/cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -march=rv64imafdc -mabi=lp64d -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-13.0-RELEASE-p11-riscv-cpython-39/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/nxb-bin/usr/bin/cc -shared -fstack-protector-strong -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-riscv-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-13.0-RELEASE-p11-riscv-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lb
 uild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-riscv-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-riscv-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): .Lline_table_start0
error: symbols defined in multiple extensions
*** Error code 1

[jmarshall]

Thanks for the report. I've further tweaked this check so that it ignores non-user-code symbols like these $foo and .bar symbols.

Tested on arm64 FreeBSD 13.1.