[package - 130arm64-default][biology/py-pysam] Failed for py38-pysam-0.19.1 in build
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Date: Sat, 18 Jun 2022 02:34:16 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://ampere3.nyi.freebsd.org/data/130arm64-default/ed9584b457ea/logs/py38-pysam-0.19.1.log
Build URL: http://ampere3.nyi.freebsd.org/build.html?mastername=130arm64-default&build=ed9584b457ea
Log:
=>> Building biology/py-pysam
build started at Sat Jun 18 02:28:48 UTC 2022
port directory: /usr/ports/biology/py-pysam
package name: py38-pysam-0.19.1
building for: FreeBSD 130arm64-default-job-04 13.0-RELEASE-p11 FreeBSD 13.0-RELEASE-p11 arm64
maintained by: yuri@FreeBSD.org
Makefile ident:
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Job Id: 04
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yuri@FreeBSD.org
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--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pysam DOCSDIR=/usr/local/share/doc/pysam EXAMPLESDIR=/usr/local/share/examples/pysam WWWDIR=/usr/local/www/pysam ETCDIR=/usr/local/etc/pysam
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py38-pysam-0.19.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5_1.pkg
[130arm64-default-job-04] Installing pkg-1.17.5_1...
[130arm64-default-job-04] Extracting pkg-1.17.5_1: .......... done
===> py38-pysam-0.19.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py38-pysam-0.19.1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py38-pysam-0.19.1 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py38-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 py38-pysam-0.19.1 for building
===> Extracting for py38-pysam-0.19.1
=> SHA256 Checksum OK for pysam-0.19.1.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py38-pysam-0.19.1
===> Applying FreeBSD patches for py38-pysam-0.19.1 from /usr/ports/biology/py-pysam/files
===========================================================================
=======================<phase: build-depends >============================
===> py38-pysam-0.19.1 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[130arm64-default-job-04] Installing gmake-4.3_2...
[130arm64-default-job-04] `-- Installing gettext-runtime-0.21...
[130arm64-default-job-04] | `-- Installing indexinfo-0.3.1...
[130arm64-default-job-04] | `-- Extracting indexinfo-0.3.1: .... done
[130arm64-default-job-04] `-- Extracting gettext-runtime-0.21: .......... done
[130arm64-default-job-04] Extracting gmake-4.3_2: .......... done
===> py38-pysam-0.19.1 depends on package: gmake>=4.3 - found
===> Returning to build of py38-pysam-0.19.1
===> py38-pysam-0.19.1 depends on executable: cython-3.8 - not found
===> Installing existing package /packages/All/py38-cython-0.29.30.pkg
[130arm64-default-job-04] Installing py38-cython-0.29.30...
[130arm64-default-job-04] `-- Installing py38-setuptools-62.1.0...
[130arm64-default-job-04] | `-- Installing python38-3.8.13_2...
[130arm64-default-job-04] | | `-- Installing libffi-3.4.2...
[130arm64-default-job-04] | | `-- Extracting libffi-3.4.2: .......... done
[130arm64-default-job-04] | | `-- Installing mpdecimal-2.5.1...
[130arm64-default-job-04] | | `-- Extracting mpdecimal-2.5.1: .......... 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-py38/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1 -I/usr/local/include/python3.8 -c pysam/libctabixproxies.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabixproxies.c:17459:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:17584:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:17701:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:17899:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18001:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18106:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18249:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18394:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18527:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18644:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18740:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18836:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18932:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:23443:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0,
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:25816:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0,
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
15 warnings generated.
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam/libctabixproxies.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm6
4-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-38 -lcutils.cpython-38 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam/libctabixproxies.cpython-38.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-py38/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1 -I/usr/local/include/python3.8 -c pysam/libcvcf.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c:31912:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libcvcf.c:32034:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libcvcf.c:32159:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libcvcf.c:38596:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0,
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libcvcf.c:40547:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0,
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
5 warnings generated.
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam/libcvcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython
-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-38 -lcutils.cpython-38 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-38/pysam/libcvcf.cpython-38.so -Wl,-rpath,$ORIGIN
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.9
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
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.4
error: symbols defined in multiple extensions
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/py-pysam