[package - main-i386-default][biology/lamarc] Failed for lamarc-2.1.8_1,1 in build
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Date: Thu, 29 Feb 2024 18:02:01 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/beefy17/data/main-i386-default/p712c7eaa68f2_s7ee47c3bb7/logs/lamarc-2.1.8_1,1.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p712c7eaa68f2_s7ee47c3bb7
Log:
=>> Building biology/lamarc
build started at Thu Feb 29 17:59:54 UTC 2024
port directory: /usr/ports/biology/lamarc
package name: lamarc-2.1.8_1,1
building for: FreeBSD main-i386-default-job-01 15.0-CURRENT FreeBSD 15.0-CURRENT 1500014 i386
maintained by: ports@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 878 Aug 19 2023 /usr/ports/biology/lamarc/Makefile
Ports top last git commit: 712c7eaa68f
Ports top unclean checkout: no
Port dir last git commit: bb82d0e6e11
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-1-g1e9f97d6
Host OSVERSION: 1500006
Jail OSVERSION: 1500014
Job Id: 01
!!! Jail is newer than host. (Jail: 1500014, Host: 1500006) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
OSVERSION=1500014
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
UNAME_m=i386
UNAME_p=i386
UNAME_r=15.0-CURRENT
LOCALBASE=/usr/local
UNAME_v=FreeBSD 15.0-CURRENT 1500014
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.1-1-g1e9f97d6
MASTERMNT=/usr/local/poudriere/data/.m/main-i386-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-i386-default/01/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-i386-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.1-1-g1e9f97d6
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for lamarc-2.1.8_1,1:
DOCS=on: Build and/or install documentation
WXGTK=off: wxGTK GUI toolkit support
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
ports@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--disable-converter --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/lamarc/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/lamarc/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/lamarc/work/.cache HOME=/wrkdirs/usr/ports/biology/lamarc/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/lamarc/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/lamarc/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/lamarc/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/lamarc/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/lamarc/work/.cache HOME=/wrkdirs/usr/ports/biology/lamarc/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/lamarc/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/lamarc/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 -std=c++98 " 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="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/lamarc" EXAMPLESDIR="share/examples/lamarc" DATADIR="share/lamarc" WWWDIR="www/lamarc" ETCDIR="etc/lamarc"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/lamarc DOCSDIR=/usr/local/share/doc/lamarc EXAMPLESDIR=/usr/local/share/examples/lamarc WWWDIR=/usr/local/www/lamarc ETCDIR=/usr/local/etc/lamarc
--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
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### ####
# 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 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
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) 524288
stack size (kbytes, -s) 65536
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) 8192
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 >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> NOTICE:
The lamarc 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 APACHE20 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> lamarc-2.1.8_1,1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.9_1.pkg
[main-i386-default-job-01] Installing pkg-1.20.9_1...
[main-i386-default-job-01] Extracting pkg-1.20.9_1: .......... done
===> lamarc-2.1.8_1,1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of lamarc-2.1.8_1,1
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> NOTICE:
The lamarc 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 APACHE20 accepted by the user
===> Fetching all distfiles required by lamarc-2.1.8_1,1 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> NOTICE:
The lamarc 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
<snip>
In file included from ./src/postlike/plforces.h:29:
In file included from ./src/tree/summary.h:30:
In file included from ./src/control/registry.h:22:
In file included from ./src/tools/random.h:15:
In file included from ./boost/random.hpp:53:
In file included from ./boost/random/random_number_generator.hpp:22:
In file included from ./boost/random/uniform_int.hpp:26:
./boost/random/uniform_smallint.hpp:39:63: warning: unused parameter 'ud' [-Wunused-parameter]
39 | InputStream& extract_uniform_int(InputStream& is, UniformInt& ud, Impl& impl)
| ^
In file included from src/report/xml_report.cpp:15:
In file included from ./src/force/force.h:16:
In file included from ./src/postlike/plforces.h:29:
./src/tree/summary.h:33:1: warning: class 'Interval' was previously declared as a struct; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
33 | class Interval;
| ^
./src/tree/intervaldata.h:55:8: note: previous use is here
55 | struct Interval
| ^
./src/tree/summary.h:33:1: note: did you mean struct here?
33 | class Interval;
| ^~~~~
| struct
./src/tree/summary.h:195:52: warning: unused parameter 'totals' [-Wunused-parameter]
195 | virtual void AdjustSummary(const DoubleVec1d & totals, long region) {};
| ^
./src/tree/summary.h:195:65: warning: unused parameter 'region' [-Wunused-parameter]
195 | virtual void AdjustSummary(const DoubleVec1d & totals, long region) {};
| ^
In file included from src/report/xml_report.cpp:15:
In file included from ./src/force/force.h:16:
./src/postlike/plforces.h:401:45: warning: unused parameter 'param' [-Wunused-parameter]
401 | double DlnWait (const vector < double >¶m,
| ^
./src/postlike/plforces.h:402:41: warning: unused parameter 'treedata' [-Wunused-parameter]
402 | const TreeSummary * treedata,
| ^
./src/postlike/plforces.h:403:33: warning: unused parameter 'whichparam' [-Wunused-parameter]
403 | const long &whichparam) { assert(false); return 0;};
| ^
./src/postlike/plforces.h:405:46: warning: unused parameter 'param' [-Wunused-parameter]
405 | double DlnPoint (const vector < double >¶m,
| ^
./src/postlike/plforces.h:406:42: warning: unused parameter 'treedata' [-Wunused-parameter]
406 | const TreeSummary * treedata,
| ^
./src/postlike/plforces.h:407:34: warning: unused parameter 'whichparam' [-Wunused-parameter]
407 | const long &whichparam) { assert(false); return 0;};
| ^
./src/postlike/plforces.h:468:44: warning: unused parameter 'param' [-Wunused-parameter]
468 | double lnWait (const vector < double >¶m,
| ^
./src/postlike/plforces.h:469:40: warning: unused parameter 'treedata' [-Wunused-parameter]
469 | const TreeSummary * treedata) { return 1.0; };
| ^
./src/postlike/plforces.h:471:45: warning: unused parameter 'param' [-Wunused-parameter]
471 | double lnPoint (const vector < double >¶m,
| ^
./src/postlike/plforces.h:472:45: warning: unused parameter 'lparam' [-Wunused-parameter]
472 | const vector < double >&lparam,
| ^
./src/postlike/plforces.h:473:41: warning: unused parameter 'treedata' [-Wunused-parameter]
473 | const TreeSummary * treedata) { return 1.0; };
| ^
./src/postlike/plforces.h:475:45: warning: unused parameter 'param' [-Wunused-parameter]
475 | double DlnWait (const vector < double >¶m,
| ^
./src/postlike/plforces.h:476:41: warning: unused parameter 'treedata' [-Wunused-parameter]
476 | const TreeSummary * treedata,
| ^
./src/postlike/plforces.h:477:33: warning: unused parameter 'whichparam' [-Wunused-parameter]
477 | const long &whichparam) { return 1.0; };
| ^
./src/postlike/plforces.h:479:46: warning: unused parameter 'param' [-Wunused-parameter]
479 | double DlnPoint (const vector < double >¶m,
| ^
./src/postlike/plforces.h:480:42: warning: unused parameter 'treedata' [-Wunused-parameter]
480 | const TreeSummary * treedata,
| ^
./src/postlike/plforces.h:481:34: warning: unused parameter 'whichparam' [-Wunused-parameter]
481 | const long &whichparam) { return 1.0; };
| ^
In file included from src/report/xml_report.cpp:15:
./src/force/force.h:256:61: warning: unused parameter 'fs' [-Wunused-parameter]
256 | virtual void ModifyEvents(const ForceSummary& fs,
| ^
./src/force/force.h:549:61: warning: unused parameter 'mystatus' [-Wunused-parameter]
549 | virtual std::string MakeStatusXML(const std::string& mystatus) const { return string(""); };
| ^
./src/force/force.h:583:61: warning: unused parameter 'mystatus' [-Wunused-parameter]
583 | virtual std::string MakeStatusXML(const std::string& mystatus) const { return string(""); };
| ^
In file included from src/report/xml_report.cpp:18:
In file included from ./src/datalike/region.h:38:
./src/tree/newick.h:46:37: warning: unused parameter 'stump' [-Wunused-parameter]
46 | virtual void ToLamarcTree(Tree& stump) { assert(false); }; // instantiating NULL tree
| ^
In file included from src/report/xml_report.cpp:19:
src/report/reportpage.h:29:1: warning: class 'PlotStruct' was previously declared as a struct; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
29 | class PlotStruct;
| ^
./src/postlike/plotstat.h:26:8: note: previous use is here
26 | struct PlotStruct
| ^
src/report/reportpage.h:29:1: note: did you mean struct here?
29 | class PlotStruct;
| ^~~~~
| struct
src/report/reportpage.h:212:10: warning: 'ProfPage::PrintTable' hides overloaded virtual function [-Woverloaded-virtual]
212 | void PrintTable(StringVec3d& wrappedtable);
| ^
src/report/reportpage.h:106:18: note: hidden overloaded virtual function 'ReportPage::PrintTable' declared here: different number of parameters (4 vs 1)
106 | virtual void PrintTable(vector<string> &colhdr, StringVec2d &rowhdr,
| ^
src/report/xml_report.cpp:39:36: warning: unused parameter 'tag' [-Wunused-parameter]
39 | force_type tag,
| ^
--- lamarc-mathx.o ---
In file included from src/tools/mathx.cpp:21:
In file included from ./src/control/registry.h:22:
In file included from ./src/tools/random.h:15:
In file included from ./boost/random.hpp:42:
In file included from ./boost/random/ranlux.hpp:21:
./boost/random/discard_block.hpp:68:38: warning: unused parameter 'x' [-Wunused-parameter]
68 | static bool validation(result_type x) { return true; } // dummy
| ^
In file included from src/tools/mathx.cpp:21:
In file included from ./src/control/registry.h:22:
In file included from ./src/tools/random.h:15:
In file included from ./boost/random.hpp:53:
In file included from ./boost/random/random_number_generator.hpp:22:
In file included from ./boost/random/uniform_int.hpp:26:
./boost/random/uniform_smallint.hpp:39:63: warning: unused parameter 'ud' [-Wunused-parameter]
39 | InputStream& extract_uniform_int(InputStream& is, UniformInt& ud, Impl& impl)
| ^
In file included from src/tools/mathx.cpp:21:
In file included from ./src/control/registry.h:24:
In file included from ./src/control/regiongammainfo.h:16:
./src/force/paramstat.h:99:59: warning: unused parameter 'ftype' [-Wunused-parameter]
99 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
| ^
./src/force/paramstat.h:100:54: warning: unused parameter 'ftype' [-Wunused-parameter]
100 | virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_identical); };
| ^
./src/force/paramstat.h:121:59: warning: unused parameter 'ftype' [-Wunused-parameter]
121 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_constant); };
| ^
./src/force/paramstat.h:122:54: warning: unused parameter 'ftype' [-Wunused-parameter]
122 | virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
| ^
./src/force/paramstat.h:163:59: warning: unused parameter 'ftype' [-Wunused-parameter]
163 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
| ^
./src/force/paramstat.h:164:54: warning: unused parameter 'ftype' [-Wunused-parameter]
164 | virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
| ^
./src/force/paramstat.h:181:59: warning: unused parameter 'ftype' [-Wunused-parameter]
181 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
| ^
./src/force/paramstat.h:182:54: warning: unused parameter 'ftype' [-Wunused-parameter]
182 | virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
| ^
./src/force/paramstat.h:201:59: warning: unused parameter 'ftype' [-Wunused-parameter]
201 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
| ^
./src/force/paramstat.h:202:54: warning: unused parameter 'ftype' [-Wunused-parameter]
202 | virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
| ^
./src/force/paramstat.h:219:59: warning: unused parameter 'ftype' [-Wunused-parameter]
219 | virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
| ^
./src/force/paramstat.h:220:54: warning: unused parameter 'ftype' [-Wunused-parameter]
220 | virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
| ^
src/tools/mathx.cpp:781:12: error: no matching function for call to 'make_pair'
781 | return std::make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/v1/__utility/pair.h:721:1: note: candidate function template not viable: expects an rvalue for 1st argument
721 | make_pair(_T1&& __t1, _T2&& __t2)
| ^ ~~~~~~~~~~
14 warnings and 1 error generated.
*** [lamarc-mathx.o] Error code 1
make[1]: stopped in /wrkdirs/usr/ports/biology/lamarc/work/lamarc-2.1.8
--- lamarc-xml_report.o ---
76 warnings generated.
mv -f .deps/lamarc-xml_report.Tpo .deps/lamarc-xml_report.Po
--- lamarc-reportpage.o ---
72 warnings generated.
mv -f .deps/lamarc-reportpage.Tpo .deps/lamarc-reportpage.Po
make[1]: 1 error
make[1]: stopped in /wrkdirs/usr/ports/biology/lamarc/work/lamarc-2.1.8
===> 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/lamarc