[package - main-armv6-default][biology/paml] Failed for paml-4.10.6 in build
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Date: Tue, 16 May 2023 04:53:57 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/p2acd86f93d11_s816129210a/logs/paml-4.10.6.log
Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=main-armv6-default&build=p2acd86f93d11_s816129210a
Log:
=>> Building biology/paml
build started at Tue May 16 04:53:43 UTC 2023
port directory: /usr/ports/biology/paml
package name: paml-4.10.6
building for: FreeBSD main-armv6-default-job-12 14.0-CURRENT FreeBSD 14.0-CURRENT 1400088 arm
maintained by: jrm@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400078
Jail OSVERSION: 1400088
Job Id: 12
!!! Jail is newer than host. (Jail: 1400088, Host: 1400078) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1400088
UNAME_v=FreeBSD 14.0-CURRENT 1400088
UNAME_r=14.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
QEMU_EMULATING=1
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-23-ga7f8d188
MASTERMNT=/usr/local/poudriere/data/.m/main-armv6-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=main-armv6-default
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OLDPWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p
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POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---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--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
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
--End CONFIGURE_ENV--
--MAKE_ENV--
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 MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT
="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
PORTDOCS="" PORTEXAMPLES="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/paml" EXAMPLESDIR="share/examples/paml" DATADIR="share/paml" WWWDIR="www/paml" ETCDIR="etc/paml"
--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--
---Begin make.conf---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=arm
MACHINE_ARCH=armv6
ARCH=${MACHINE_ARCH}
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_9d218390=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: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=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: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_9d218390_58173849=yes
CC_OUTPUT_9d218390_9bdba57c=yes
CC_OUTPUT_9d218390_6a4fe7f5=yes
CC_OUTPUT_9d218390_6bcac02b=yes
CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
CC_OUTPUT_9d218390_f00456e5=yes
CC_OUTPUT_9d218390_65ad290d=yes
CC_OUTPUT_9d218390_f2776b26=yes
CC_OUTPUT_9d218390_53255a77=yes
CC_OUTPUT_9d218390_911cfe02=yes
CC_OUTPUT_9d218390_b2657cc3=yes
CC_OUTPUT_9d218390_380987f7=yes
CC_OUTPUT_9d218390_160933ec=yes
CC_OUTPUT_9d218390_fb62803b=yes
CC_OUTPUT_9d218390_af59ad06=yes
CC_OUTPUT_9d218390_a15f3fcf=yes
_OBJC_CCVERSION_9d218390=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: /nxb-bin/usr/bin
_OBJC_ALTCCVERSION_9d218390=none
ARCH=armv6
OPSYS=FreeBSD
_OSRELEASE=14.0-CURRENT
OSREL=14.0
OSVERSION=1400088
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
RANLIB=/nxb-bin/usr/bin/ranlib
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MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
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FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
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core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 1024
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<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-12] Installing pkg-1.19.1_1...
[main-armv6-default-job-12] 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-12] Installing gmake-4.3_2...
[main-armv6-default-job-12] `-- Installing gettext-runtime-0.21.1...
[main-armv6-default-job-12] | `-- Installing indexinfo-0.3.1...
[main-armv6-default-job-12] | `-- Extracting indexinfo-0.3.1: .... done
[main-armv6-default-job-12] `-- Extracting gettext-runtime-0.21.1: .......... done
[main-armv6-default-job-12] 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 0x04745d04 0x4745d04 0x4743ba0
#1 0x04745d04 0x46ed2dc 0x46ed49c
#2 0x04745d04 (+0x4745d04)
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 0x04745d04 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 0x04743ba0 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 0x046ed2dc 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 0x046ed49c 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 0xf4e6f4ec 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-40984a.c
cc: note: diagnostic msg: /tmp/baseml-40984a.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