[package - main-i386-default][biology/haplohseq] Failed for haplohseq-0.1.2_8 in build
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Date: Sat, 08 Jul 2023 13:17:17 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: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p7d33ce06c059_s884eaacd24/logs/haplohseq-0.1.2_8.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p7d33ce06c059_s884eaacd24
Log:
=>> Building biology/haplohseq
build started at Sat Jul 8 13:17:04 UTC 2023
port directory: /usr/ports/biology/haplohseq
package name: haplohseq-0.1.2_8
building for: FreeBSD main-i386-default-job-03 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 i386
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400093
Job Id: 03
!!! 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. !!!
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---Begin OPTIONS List---
===> The following configuration options are available for haplohseq-0.1.2_8:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/haplohseq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/haplohseq/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/haplohseq/work/.cache HOME=/wrkdirs/usr/ports/biology/haplohseq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/haplohseq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/haplohseq/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
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--End PLIST_SUB--
--SUB_LIST--
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> haplohseq-0.1.2_8 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.2.pkg
[main-i386-default-job-03] Installing pkg-1.19.2...
[main-i386-default-job-03] Extracting pkg-1.19.2: .......... done
===> haplohseq-0.1.2_8 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of haplohseq-0.1.2_8
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by haplohseq-0.1.2_8 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by haplohseq-0.1.2_8 for building
=> SHA256 Checksum OK for outpaddling-haplohseq-0.1.2_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by haplohseq-0.1.2_8 for building
===> Extracting for haplohseq-0.1.2_8
=> SHA256 Checksum OK for outpaddling-haplohseq-0.1.2_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for haplohseq-0.1.2_8
===> Applying FreeBSD patches for haplohseq-0.1.2_8 from /usr/ports/biology/haplohseq/files
===========================================================================
=======================<phase: build-depends >============================
===> haplohseq-0.1.2_8 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[main-i386-default-job-03] Installing gmake-4.3_2...
[main-i386-default-job-03] `-- Installing gettext-runtime-0.21.1...
[main-i386-default-job-03] | `-- Installing indexinfo-0.3.1...
[main-i386-default-job-03] | `-- Extracting indexinfo-0.3.1: .... done
[main-i386-default-job-03] `-- Extracting gettext-runtime-0.21.1: .......... done
[main-i386-default-job-03] Extracting gmake-4.3_2: .......... done
===> haplohseq-0.1.2_8 depends on package: gmake>=4.3 - found
===> Returning to build of haplohseq-0.1.2_8
===> haplohseq-0.1.2_8 depends on file: /usr/local/bin/python3.9 - not found
===> Installing existing package /packages/All/python39-3.9.17.pkg
[main-i386-default-job-03] Installing python39-3.9.17...
[main-i386-default-job-03] `-- Installing libffi-3.4.4...
[main-i386-default-job-03] `-- Extracting libffi-3.4.4: .......... done
[main-i386-default-job-03] `-- Installing mpdecimal-2.5.1...
[main-i386-default-job-03] `-- Extracting mpdecimal-2.5.1: .......... done
[main-i386-default-job-03] `-- Installing readline-8.2.1...
[main-i386-default-job-03] `-- Extracting readline-8.2.1: .......... done
[main-i386-default-job-03] Extracting python39-3.9.17: .......... done
=====
Message from python39-3.9.17:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> haplohseq-0.1.2_8 depends on file: /usr/local/bin/python3.9 - found
===> Returning to build of haplohseq-0.1.2_8
===========================================================================
=======================<phase: lib-depends >============================
===> haplohseq-0.1.2_8 depends on shared library: libboost_system.so - not found
===> Installing existing package /packages/All/boost-libs-1.82.0_1.pkg
[main-i386-default-job-03] Installing boost-libs-1.82.0_1...
[main-i386-default-job-03] `-- Installing icu-73.2,1...
[main-i386-default-job-03] `-- Extracting icu-73.2,1: .......... done
[main-i386-default-job-03] Extracting boost-libs-1.82.0_1: .......... done
=====
Message from boost-libs-1.82.0_1:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> haplohseq-0.1.2_8 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so)
===> Returning to build of haplohseq-0.1.2_8
===========================================================================
=======================<phase: configure >============================
===> Configuring for haplohseq-0.1.2_8
===========================================================================
=======================<phase: build >============================
===> Building for haplohseq-0.1.2_8
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/haplohseq/work/haplohseq-0.1.2'
mkdir -p build build/bin build/obj
mkdir -p build/test
cp -r src/test/resources build/test
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Hmm.o src/hmm/Hmm.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/DataStructures.o src/hmm/DataStructures.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/MathUtil.o src/hmm/MathUtil.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/StringUtil.o src/util/StringUtil.cpp
src/util/StringUtil.cpp:51:76: error: no member named 'ptr_fun' in namespace 'std'
s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun<int, int>(std::isspace))));
~~~~~^
src/util/StringUtil.cpp:51:87: error: expected '(' for function-style cast or type construction
s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun<int, int>(std::isspace))));
~~~^
src/util/StringUtil.cpp:51:92: error: expected '(' for function-style cast or type construction
s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun<int, int>(std::isspace))));
~~~^
src/util/StringUtil.cpp:57:67: error: no member named 'ptr_fun' in namespace 'std'
s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
~~~~~^
src/util/StringUtil.cpp:57:78: error: expected '(' for function-style cast or type construction
s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
~~~^
src/util/StringUtil.cpp:57:83: error: expected '(' for function-style cast or type construction
s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
~~~^
6 errors generated.
gmake[1]: *** [makefile:51: build/obj/StringUtil.o] Error 1
gmake[1]: *** Waiting for unfinished jobs....
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/haplohseq/work/haplohseq-0.1.2'
===> 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/haplohseq