[package - main-amd64-default][biology/lamarc] Failed for lamarc-2.1.8_1,1 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Sat, 22 Jun 2024 05:52:31 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/beefy18/data/main-amd64-default/pf558721194b8_s42c545c5f8a/logs/lamarc-2.1.8_1,1.log
Build URL:      https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=pf558721194b8_s42c545c5f8a
Log:

=>> Building biology/lamarc
build started at Sat Jun 22 05:50:32 UTC 2024
port directory: /usr/ports/biology/lamarc
package name: lamarc-2.1.8_1,1
building for: FreeBSD main-amd64-default-job-10 15.0-CURRENT FreeBSD 15.0-CURRENT 1500019 amd64
maintained by: ports@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root wheel 878 Aug 20  2023 /usr/ports/biology/lamarc/Makefile
Ports top last git commit: f558721194b
Ports top unclean checkout: no
Port dir last git commit: bb82d0e6e11
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500018
Jail OSVERSION: 1500019
Job Id: 10




!!! Jail is newer than host. (Jail: 1500019, Host: 1500018) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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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---
# 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
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
####  ####
# 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)  33554432
stack size              (kbytes, -s)  524288
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-1.21.3.pkg
[main-amd64-default-job-10] Installing pkg-1.21.3...
[main-amd64-default-job-10] Extracting pkg-1.21.3: .......... 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:
<snip>
In file included from src/report/xml_report.cpp:15:
In file included from ./src/force/force.h:15:
In file included from ./src/tree/parameter.h:66:
./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); };
      |                                                      ^
--- lamarc-mathx.o ---
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:599:5: note: candidate function template not viable: expects an rvalue for 1st argument
  599 |     make_pair(_T1&& __t1, _T2&& __t2) {
      |     ^         ~~~~~~~~~~
--- lamarc-xml_report.o ---
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:
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: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/report/xml_report.cpp:15:
In file included from ./src/force/force.h:16:
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 >&param,
      |                                             ^
./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 >&param,
      |                                              ^
./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 >&param,
      |                                            ^
./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 >&param,
      |                                             ^
./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 >&param,
      |                                             ^
./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 >&param,
      |                                              ^
./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; };
      |                                  ^
--- lamarc-mathx.o ---
14 warnings and 1 error generated.
--- lamarc-xml_report.o ---
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,
      |                                                             ^
--- lamarc-mathx.o ---
*** [lamarc-mathx.o] Error code 1

make: stopped in /wrkdirs/usr/ports/biology/lamarc/work/lamarc-2.1.8
--- lamarc-xml_report.o ---
./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,
      |                                    ^
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 error

make: 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