[package - main-armv6-default][biology/bamutil] Failed for bamutil-1.0.15 in build
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Date: Thu, 30 Mar 2023 08:57:38 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: https://pkg-status.freebsd.org/beefy8/data/main-armv6-default/pa097efdbe2f4_s1fb7d2cf99/logs/bamutil-1.0.15.log
Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=main-armv6-default&build=pa097efdbe2f4_s1fb7d2cf99
Log:
=>> Building biology/bamutil
build started at Thu Mar 30 08:57:25 UTC 2023
port directory: /usr/ports/biology/bamutil
package name: bamutil-1.0.15
building for: FreeBSD main-armv6-default-job-05 14.0-CURRENT FreeBSD 14.0-CURRENT 1400085 arm
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400078
Jail OSVERSION: 1400085
Job Id: 05
!!! Jail is newer than host. (Jail: 1400085, Host: 1400078) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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jwb@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-armv6-default-job-05] Installing pkg-1.19.1_1...
[main-armv6-default-job-05] Extracting pkg-1.19.1_1: .......... done
===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bamutil-1.0.15
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bamutil-1.0.15 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bamutil-1.0.15 for building
=> SHA256 Checksum OK for statgen-bamUtil-v1.0.15_GH0.tar.gz.
=> SHA256 Checksum OK for statgen-libStatGen-v1.0.15_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bamutil-1.0.15 for building
===> Extracting for bamutil-1.0.15
=> SHA256 Checksum OK for statgen-bamUtil-v1.0.15_GH0.tar.gz.
=> SHA256 Checksum OK for statgen-libStatGen-v1.0.15_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for bamutil-1.0.15
===> Applying FreeBSD patches for bamutil-1.0.15 from /usr/ports/biology/bamutil/files
===========================================================================
=======================<phase: build-depends >============================
===> bamutil-1.0.15 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[main-armv6-default-job-05] Installing gmake-4.3_2...
[main-armv6-default-job-05] `-- Installing gettext-runtime-0.21.1...
[main-armv6-default-job-05] | `-- Installing indexinfo-0.3.1...
[main-armv6-default-job-05] | `-- Extracting indexinfo-0.3.1: .... done
[main-armv6-default-job-05] `-- Extracting gettext-runtime-0.21.1: .......... done
[main-armv6-default-job-05] Extracting gmake-4.3_2: .......... done
===> bamutil-1.0.15 depends on package: gmake>=4.3 - found
===> Returning to build of bamutil-1.0.15
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for bamutil-1.0.15
===========================================================================
=======================<phase: build >============================
===> Building for bamutil-1.0.15
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15'
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/src'
gmake -C /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen --no-print-directory opt
ln -s ../samtools/bgzf.h ../include/bgzf.h
ln -s ../samtools/knetfile.h ../include/knetfile.h
ln -s ../samtools/khash.h ../include/khash.h
ln -s ../samtools/bam.h ../include/bam.h
mkdir -p obj
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/bgzf.o -c bgzf.c
PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script.
Stack dump:
0. Program arguments: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -strict-aliasing -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/bgzf.o bgzf.c
1. <eof> parser at end of file
2. Code generation
#0 0x04746b54 0x4746b54 0x47449f0
#1 0x04746b54 0x46ee12c 0x46ee2ec
#2 0x04746b54 (+0x4746b54)
Stack dump without symbol names (ensure you have llvm-symbolizer in your PATH or set the environment var `LLVM_SYMBOLIZER_PATH` to point to it):
0 cc 0x04746b54 std::__1::enable_if<__is_cpp17_forward_iterator<char const*>::value, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&>::type std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>::append[abi:v15007]<char const*>(char const*, char const*) + 2574684
1 cc 0x047449f0 std::__1::enable_if<__is_cpp17_forward_iterator<char const*>::value, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&>::type std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>::append[abi:v15007]<char const*>(char const*, char const*) + 2566136
2 cc 0x046ee12c std::__1::enable_if<__is_cpp17_forward_iterator<char const*>::value, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&>::type std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>::append[abi:v15007]<char const*>(char const*, char const*) + 2211636
3 cc 0x046ee2ec std::__1::enable_if<__is_cpp17_forward_iterator<char const*>::value, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&>::type std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>::append[abi:v15007]<char const*>(char const*, char const*) + 2212084
4 libthr.so.3 0xf4e6f454 pthread_sigmask + 1448
cc: error: clang frontend command failed with exit code 139 (use -v to see invocation)
qemu: uncaught target signal 4 (Illegal instruction) - core dumped
gmake[4]: *** [../Makefiles/Makefile.common:74: obj/bgzf.o] Illegal instruction
gmake[3]: *** [Makefiles/Makefile.base:15: samtools] Error 2
gmake[2]: *** [/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/Makefiles/Makefile.ext:50: /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/libStatGen.a] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/src'
gmake[1]: *** [/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/Makefiles/Makefile.base:15: src] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/bamutil