[package - main-riscv64-default][biology/stacks] Failed for stacks-2.4_2 in build

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From: <pkg-fallout_at_FreeBSD.org>
Date: Thu, 12 Aug 2021 17:56:33 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:     jwb@FreeBSD.org
Log URL:        http://beefy7.nyi.freebsd.org/data/main-riscv64-default/p507d4271e0bb_sa3ff18e271/logs/stacks-2.4_2.log
Build URL:      http://beefy7.nyi.freebsd.org/build.html?mastername=main-riscv64-default&build=p507d4271e0bb_sa3ff18e271
Log:

=>> Building biology/stacks
build started at Thu Aug 12 17:55:21 UTC 2021
port directory: /usr/ports/biology/stacks
package name: stacks-2.4_2
building for: FreeBSD main-riscv64-default-job-01 14.0-CURRENT FreeBSD 14.0-CURRENT 1400029 riscv
maintained by: jwb@FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400008
Jail OSVERSION: 1400029
Job Id: 01




!!! Jail is newer than host. (Jail: 1400029, Host: 1400008) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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=======================<phase: check-sanity   >============================
===>  License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   stacks-2.4_2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.17.1.pkg
[main-riscv64-default-job-01] Installing pkg-1.17.1...
[main-riscv64-default-job-01] Extracting pkg-1.17.1: .......... done
===>   stacks-2.4_2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of stacks-2.4_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by stacks-2.4_2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by stacks-2.4_2 for building
<snip>
checking for ar... ar
checking the archiver (ar) interface... ar
checking for omp_set_num_threads in -lgomp... yes
checking for gzread in -lz... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking how to run the C preprocessor... /nxb-bin/usr/bin/cpp
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
checking for ANSI C header files... (cached) yes
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for float.h... (cached) yes
checking for limits.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for /nxb-bin/usr/bin/cc option to support OpenMP... -fopenmp
checking for stdbool.h that conforms to C99... (cached) yes
checking for _Bool... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... (cached) yes
checking whether closedir returns void... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for floor... no
checking for memset... (cached) yes
checking for pow... no
checking for sqrt... no
checking for clock_gettime... (cached) yes
checking for functional regular expressions... yes
checking for gawk... (cached) /usr/bin/awk
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating htslib/Makefile
config.status: creating config.h
config.status: executing depfiles commands
===========================================================================
=======================<phase: build          >============================
===>  Building for stacks-2.4_2
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4'
gmake  all-recursive
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4'
Making all in htslib
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4/htslib'
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/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT hfile.o -MD -MP -MF $depbase.Tpo -c -o hfile.o hfile.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo hfile_net.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT hfile_net.o -MD -MP -MF $depbase.Tpo -c -o hfile_net.o hfile_net.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo hts.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT hts.o -MD -MP -MF $depbase.Tpo -c -o hts.o hts.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo hts_os.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT hts_os.o -MD -MP -MF $depbase.Tpo -c -o hts_os.o hts_os.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo htsfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT htsfile.o -MD -MP -MF $depbase.Tpo -c -o htsfile.o htsfile.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo kfunc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT kfunc.o -MD -MP -MF $depbase.Tpo -c -o kfunc.o kfunc.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo knetfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT knetfile.o -MD -MP -MF $depbase.Tpo -c -o knetfile.o knetfile.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo kstring.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT kstring.o -MD -MP -MF $depbase.Tpo -c -o kstring.o kstring.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo md5.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT md5.o -MD -MP -MF $depbase.Tpo -c -o md5.o md5.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo multipart.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT multipart.o -MD -MP -MF $depbase.Tpo -c -o multipart.o multipart.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo os/rand.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT os/rand.o -MD -MP -MF $depbase.Tpo -c -o os/rand.o os/rand.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo probaln.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT probaln.o -MD -MP -MF $depbase.Tpo -c -o probaln.o probaln.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo realn.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT realn.o -MD -MP -MF $depbase.Tpo -c -o realn.o realn.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo regidx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT regidx.o -MD -MP -MF $depbase.Tpo -c -o regidx.o regidx.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo sam.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT sam.o -MD -MP -MF $depbase.Tpo -c -o sam.o sam.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo synced_bcf_reader.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT synced_bcf_reader.o -MD -MP -MF $depbase.Tpo -c -o synced_bcf_reader.o synced_bcf_reader.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo tabix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT tabix.o -MD -MP -MF $depbase.Tpo -c -o tabix.o tabix.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo tbx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT tbx.o -MD -MP -MF $depbase.Tpo -c -o tbx.o tbx.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo textutils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT textutils.o -MD -MP -MF $depbase.Tpo -c -o textutils.o textutils.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo thread_pool.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT thread_pool.o -MD -MP -MF $depbase.Tpo -c -o thread_pool.o thread_pool.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo vcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT vcf.o -MD -MP -MF $depbase.Tpo -c -o vcf.o vcf.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo vcf_sweep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT vcf_sweep.o -MD -MP -MF $depbase.Tpo -c -o vcf_sweep.o vcf_sweep.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo vcfutils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/cc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=rv64imafdc -mabi=lp64d  -fstack-protector-strong -fno-strict-aliasing  -MT vcfutils.o -MD -MP -MF $depbase.Tpo -c -o vcfutils.o vcfutils.c &&\
mv -f $depbase.Tpo $depbase.Po
rm -f libhts.a
ar cru libhts.a bcf_sr_sort.o bgzf.o bgzip.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o htsfile.o kfunc.o knetfile.o kstring.o md5.o multipart.o os/rand.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o tabix.o tbx.o textutils.o thread_pool.o vcf.o vcf_sweep.o vcfutils.o 
ranlib libhts.a
Assertion failed: (mode == 'p' || mode == 't' || mode == 'x'), function ar_read_archive, file /usr/local/poudriere/jails/main-riscv64/usr/src/usr.bin/ar/read.c, line 68.
qemu: uncaught target signal 6 (Abort trap) - core dumped
gmake[3]: *** [Makefile:457: libhts.a] Abort trap
gmake[3]: *** Deleting file 'libhts.a'
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4/htslib'
gmake[2]: *** [Makefile:1053: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4'
gmake[1]: *** [Makefile:704: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.4'
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/stacks