[package - main-arm64-default][biology/primer3] Failed for primer3-2.3.6 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Sun, 23 Jul 2023 03:25:02 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: ports@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/pe5b71726cc79_s92fd2f39e5/logs/primer3-2.3.6.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=pe5b71726cc79_s92fd2f39e5
Log:
=>> Building biology/primer3
build started at Sun Jul 23 03:24:44 UTC 2023
port directory: /usr/ports/biology/primer3
package name: primer3-2.3.6
building for: FreeBSD main-arm64-default-job-09 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 arm64
maintained by: ports@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400093
Job Id: 09
!!! Jail is newer than host. (Jail: 1400093, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1400093
UNAME_v=FreeBSD 14.0-CURRENT 1400093
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
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-23-ga7f8d188
MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=main-arm64-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
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---
---End OPTIONS List---
--MAINTAINER--
ports@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/primer3/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/primer3/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/primer3/work/.cache HOME=/wrkdirs/usr/ports/biology/primer3/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/primer3/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/primer3/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/primer3/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/primer3/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/primer3/work/.cache HOME=/wrkdirs/usr/ports/biology/primer3/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/primer3/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/primer3/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="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="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_D
ATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/primer3" EXAMPLESDIR="share/examples/primer3" DATADIR="share/primer3" WWWDIR="www/primer3" ETCDIR="etc/primer3"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/primer3 DOCSDIR=/usr/local/share/doc/primer3 EXAMPLESDIR=/usr/local/share/examples/primer3 WWWDIR=/usr/local/www/primer3 ETCDIR=/usr/local/etc/primer3
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### /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_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--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_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_53255a77=yes
CC_OUTPUT_921dbbb2_911cfe02=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
CC_OUTPUT_921dbbb2_af59ad06=yes
CC_OUTPUT_921dbbb2_a15f3fcf=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=aarch64
OPSYS=FreeBSD
_OSRELEASE=14.0-CURRENT
OSREL=14.0
OSVERSION=1400093
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 1048576
stack size (kbytes, -s) 1048576
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 >============================
===> NOTICE:
The primer3 port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> primer3-2.3.6 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[main-arm64-default-job-09] Installing pkg-1.20.4...
[main-arm64-default-job-09] Extracting pkg-1.20.4: .......... done
===> primer3-2.3.6 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of primer3-2.3.6
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> NOTICE:
The primer3 port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by primer3-2.3.6 for building
===========================================================================
=======================<phase: checksum >============================
===> NOTICE:
The primer3 port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by primer3-2.3.6 for building
=> SHA256 Checksum OK for primer3-src-2.3.6.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> NOTICE:
The primer3 port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by primer3-2.3.6 for building
===> Extracting for primer3-2.3.6
=> SHA256 Checksum OK for primer3-src-2.3.6.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for primer3-2.3.6
===> Applying FreeBSD patches for primer3-2.3.6 from /usr/ports/biology/primer3/files
===========================================================================
=======================<phase: build-depends >============================
===> primer3-2.3.6 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[main-arm64-default-job-09] Installing gmake-4.3_2...
[main-arm64-default-job-09] `-- Installing gettext-runtime-0.22_1...
[main-arm64-default-job-09] | `-- Installing indexinfo-0.3.1...
[main-arm64-default-job-09] | `-- Extracting indexinfo-0.3.1: .... done
[main-arm64-default-job-09] `-- Extracting gettext-runtime-0.22_1: .......... done
[main-arm64-default-job-09] Extracting gmake-4.3_2: .......... done
===> primer3-2.3.6 depends on package: gmake>=4.3 - found
===> Returning to build of primer3-2.3.6
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for primer3-2.3.6
===========================================================================
=======================<phase: build >============================
===> Building for primer3-2.3.6
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/primer3/work/primer3-2.3.6/src'
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ primer3_boulder_main.c
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o format_output.o format_output.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
format_output.c:418:48: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare]
if (pa->pick_right_primer && &retval->rev != NULL
~~~~~~~~^~~ ~~~~
format_output.c:429:47: warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare]
if (pa->pick_left_primer && &retval->fwd != NULL
~~~~~~~~^~~ ~~~~
format_output.c:851:45: warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare]
if ((pa->pick_left_primer) && (&retval->fwd != NULL )
~~~~~~~~^~~ ~~~~
format_output.c:858:48: warning: comparison of address of 'retval->intl' not equal to a null pointer is always true [-Wtautological-pointer-compare]
if ((pa->pick_internal_oligo) && (&retval->intl != NULL )
~~~~~~~~^~~~ ~~~~
format_output.c:865:46: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare]
if ((pa->pick_right_primer) && (&retval->rev != NULL )
~~~~~~~~^~~ ~~~~
format_output.c:888:43: warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare]
if ((pa->pick_left_primer) && (&retval->fwd != NULL )
~~~~~~~~^~~ ~~~~
format_output.c:907:46: warning: comparison of address of 'retval->intl' not equal to a null pointer is always true [-Wtautological-pointer-compare]
if ((pa->pick_internal_oligo) && (&retval->intl != NULL )
~~~~~~~~^~~~ ~~~~
format_output.c:926:44: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare]
if ((pa->pick_right_primer) && (&retval->rev != NULL )
~~~~~~~~^~~ ~~~~
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o read_boulder.o read_boulder.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
8 warnings generated.
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o print_boulder.o print_boulder.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -Wno-deprecated -o libprimer3.o libprimer3.c
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o p3_seq_lib.o p3_seq_lib.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o dpal_primer.o dpal.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j, k, mg, c;
^~~~~~~~~
dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j, k, mg, c;
^~~~~~~~~
dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j, k, mg, c;
^~~~~~~~~
dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j, k, mg, c;
^~~~~~~~~
dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j, k, mg, c;
^~~~~~~~~
dpal.c:369:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
^~~~~~~~~
dpal.c:369:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
^~~~~~~~~
dpal.c:369:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j, k, mg, mgy, c;
^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j, k, mg, mgy, c;
^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j, k, mg, mgy, c;
^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j, k, mg, mgy, c;
^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j, k, mg, mgy, c;
^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j, k, mg, mgy, c;
^~~~~~~~~
dpal.c:595:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
^~~~~~~~~
dpal.c:595:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
^~~~~~~~~
dpal.c:595:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
^~~~~~~~~
dpal.c:760:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j;
^~~~~~~~~
dpal.c:760:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
register int i, j;
^~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
gmake[1]: *** [Makefile:189: dpal_primer.o] Error 1
gmake[1]: *** Waiting for unfinished jobs....
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/primer3/work/primer3-2.3.6/src'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/primer3