[package - main-armv6-default][biology/paml] Failed for paml-4.10.6 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Sat, 08 Apr 2023 05:04:14 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:     jrm@FreeBSD.org
Log URL:        https://pkg-status.freebsd.org/beefy8/data/main-armv6-default/pdbf7b69ad1dc_s182b21d462/logs/paml-4.10.6.log
Build URL:      https://pkg-status.freebsd.org/beefy8/build.html?mastername=main-armv6-default&build=pdbf7b69ad1dc_s182b21d462
Log:

=>> Building biology/paml
build started at Sat Apr  8 05:04:00 UTC 2023
port directory: /usr/ports/biology/paml
package name: paml-4.10.6
building for: FreeBSD main-armv6-default-job-08 14.0-CURRENT FreeBSD 14.0-CURRENT 1400085 arm
maintained by: jrm@FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400078
Jail OSVERSION: 1400085
Job Id: 08




!!! 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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---Begin OPTIONS List---
===> The following configuration options are available for paml-4.10.6:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
jrm@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

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MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/paml/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/paml/work  XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/paml/work/.cache  HOME=/wrkdirs/usr/ports/biology/paml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/paml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/paml/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/paml DOCSDIR=/usr/local/share/doc/paml EXAMPLESDIR=/usr/local/share/examples/paml  WWWDIR=/usr/local/www/paml ETCDIR=/usr/local/etc/paml
--End SUB_LIST--

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=======================<phase: check-sanity   >============================
===>  License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   paml-4.10.6 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-armv6-default-job-08] Installing pkg-1.19.1_1...
[main-armv6-default-job-08] Extracting pkg-1.19.1_1: .......... done
===>   paml-4.10.6 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of paml-4.10.6
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by paml-4.10.6 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by paml-4.10.6 for building
=> SHA256 Checksum OK for abacus-gene-paml-v4.10.6_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by paml-4.10.6 for building
===>  Extracting for paml-4.10.6
=> SHA256 Checksum OK for abacus-gene-paml-v4.10.6_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for paml-4.10.6
===>   Converting DOS text files to UNIX text files
===========================================================================
=======================<phase: build-depends  >============================
===>   paml-4.10.6 depends on package: gmake>=4.3 - not found
===>   Installing existing package /packages/All/gmake-4.3_2.pkg
[main-armv6-default-job-08] Installing gmake-4.3_2...
[main-armv6-default-job-08] `-- Installing gettext-runtime-0.21.1...
[main-armv6-default-job-08] |   `-- Installing indexinfo-0.3.1...
[main-armv6-default-job-08] |   `-- Extracting indexinfo-0.3.1: .... done
[main-armv6-default-job-08] `-- Extracting gettext-runtime-0.21.1: .......... done
[main-armv6-default-job-08] Extracting gmake-4.3_2: .......... done
===>   paml-4.10.6 depends on package: gmake>=4.3 - found
===>   Returning to build of paml-4.10.6
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for paml-4.10.6
===========================================================================
=======================<phase: build          >============================
===>  Building for paml-4.10.6
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/paml/work/paml-4.10.6/src'
cc  -O3 -Wall -Wno-unused-result -c baseml.c
In file included from baseml.c:137:
./treesub.c:2993:19: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
      if (line[i] == EOF)
          ~~~~~~~ ^  ~~~
./treesub.c:4606:8: warning: variable 'step' set but not used [-Wunused-but-set-variable]
   int step = 0, ntree = 0, nmove = 0, improve = 0, ineighb, i;
       ^
./treesub.c:6257:35: warning: variable 'nchange' set but not used [-Wunused-but-set-variable]
   int nid = tree.nnode - com.ns, nchange;
                                  ^
Assertion failed: (isStringAttribute() && "Invalid attribute type to get the value as a string!"), function getValueAsString, file /usr/local/poudriere/jails/main-armv6/usr/src/contrib/llvm-project/llvm/lib/IR/Attributes.cpp, line 307.
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 -O3 -Wall -Wno-unused-result -c baseml.c
1.	<eof> parser at end of file
2.	Optimizer
#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 134 (use -v to see invocation)
FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6)
Target: armv6-unknown-freebsd14.0-gnueabihf
Thread model: posix
InstalledDir: /usr/bin
cc: note: diagnostic msg: 
********************

PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
cc: note: diagnostic msg: /tmp/baseml-5b7c85.c
cc: note: diagnostic msg: /tmp/baseml-5b7c85.sh
cc: note: diagnostic msg: 

********************
gmake[1]: *** [Makefile:32: baseml.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/paml/work/paml-4.10.6/src'
*** Error code 2

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