[package - 143amd64-default][biology/viennarna] Failed for viennarna-2.7.0_1 in build
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Date: Tue, 07 Oct 2025 01:48:44 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy22/data/143amd64-default/9ab81a2c7468/logs/viennarna-2.7.0_1.log
Build URL: https://pkg-status.freebsd.org/beefy22/build.html?mastername=143amd64-default&build=9ab81a2c7468
Log:
=>> Building biology/viennarna
build started at Tue Oct 7 01:45:44 -00 2025
port directory: /usr/ports/biology/viennarna
package name: viennarna-2.7.0_1
building for: FreeBSD 143amd64-default-job-22 14.3-RELEASE-p4 FreeBSD 14.3-RELEASE-p4 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 2053 Jul 24 01:01 /usr/ports/biology/viennarna/Makefile
Ports top last git commit: 9ab81a2c74
Ports top unclean checkout: no
Port dir last git commit: 15209a6774
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.3-6-gb115e081
Host OSVERSION: 1600000
Jail OSVERSION: 1403000
Job Id: 22
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===> The following configuration options are available for viennarna-2.7.0_1:
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--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--enable-shared --disable-static --with-gsl --with-cluster --with-kinwalker --enable-mpfr --without-python --without-python3 --without-perl --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
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#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
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max memory size (kbytes, -m) unlimited
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--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License ViennaRNALicense accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> viennarna-2.7.0_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.3.1.pkg
[143amd64-default-job-22] Installing pkg-2.3.1...
[143amd64-default-job-22] Extracting pkg-2.3.1: .......... done
===> viennarna-2.7.0_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of viennarna-2.7.0_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
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.7.0_1 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.7.0_1 for building
=> SHA256 Checksum OK for ViennaRNA-2.7.0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.7.0_1 for building
===> Extracting for viennarna-2.7.0_1
=> SHA256 Checksum OK for ViennaRNA-2.7.0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for viennarna-2.7.0_1
===> Applying FreeBSD patches for viennarna-2.7.0_1 from /usr/ports/biology/viennarna/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> viennarna-2.7.0_1 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.3.3_1.pkg
[143amd64-default-job-22] Installing bash-5.3.3_1...
[143amd64-default-job-22] `-- Installing gettext-runtime-0.23.1...
[143amd64-default-job-22] | `-- Installing indexinfo-0.3.1_1...
[143amd64-default-job-22] | `-- Extracting indexinfo-0.3.1_1: .... done
[143amd64-default-job-22] `-- Extracting gettext-runtime-0.23.1: .......... done
[143amd64-default-job-22] Extracting bash-5.3.3_1: .......... done
===> viennarna-2.7.0_1 depends on executable: bash - found
===> Returning to build of viennarna-2.7.0_1
===> viennarna-2.7.0_1 depends on package: lapacke>0 - not found
===> Installing existing package /packages/All/lapacke-3.12.1.pkg
[143amd64-default-job-22] Installing lapacke-3.12.1...
[143amd64-default-job-22] `-- Installing blas-3.12.1...
[143amd64-default-job-22] | `-- Installing gcc13-13.3.0_3...
[143amd64-default-job-22] | | `-- Installing binutils-2.44,1...
[143amd64-default-job-22] | | `-- Installing zstd-1.5.7...
[143amd64-default-job-22] | | | `-- Installing liblz4-1.10.0,1...
[143amd64-default-job-22] | | | `-- Extracting liblz4-1.10.0,1: .......... done
[143amd64-default-job-22] | | `-- Extracting zstd-1.5.7: .......... done
<snip>
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2911:3: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2911 | traits_type::assign(*__p, __c);
| ^
../dlib-19.24/dlib/all/../bigint/../unicode/unicode.h:509:18: note: in instantiation of member function 'std::basic_string<unsigned int>::push_back' requested here
509 | temp.push_back(ch);
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2912:3: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2912 | traits_type::assign(*++__p, value_type());
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2535:5: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2535 | traits_type::copy(std::__to_address(__p), std::__to_address(__old_p), __n_copy);
| ^
/usr/include/c++/v1/string:2556:3: note: in instantiation of member function 'std::basic_string<unsigned int>::__grow_by' requested here
2556 | __grow_by(__old_cap, __delta_cap, __old_sz, __n_copy, __n_del, __n_add);
| ^
/usr/include/c++/v1/string:2898:5: note: in instantiation of member function 'std::basic_string<unsigned int>::__grow_by_without_replace' requested here
2898 | __grow_by_without_replace(__cap, 1, __sz, __sz, 0);
| ^
../dlib-19.24/dlib/all/../bigint/../unicode/unicode.h:509:18: note: in instantiation of member function 'std::basic_string<unsigned int>::push_back' requested here
509 | temp.push_back(ch);
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2538:5: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2538 | traits_type::copy(
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2861:5: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2861 | traits_type::assign(std::__to_address(__p) + __sz, __n, __c);
| ^
/usr/include/c++/v1/string:3302:5: note: in instantiation of member function 'std::basic_string<unsigned int>::append' requested here
3302 | append(__n - __sz, __c);
| ^
/usr/include/c++/v1/string:1303:84: note: in instantiation of member function 'std::basic_string<unsigned int>::resize' requested here
1303 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 void resize(size_type __n) { resize(__n, value_type()); }
| ^
../dlib-19.24/dlib/all/../bigint/../serialize.h:2011:14: note: in instantiation of member function 'std::basic_string<unsigned int>::resize' requested here
2011 | item.resize(size);
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2864:5: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2864 | traits_type::assign(__p[__sz], value_type());
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2221:5: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2221 | traits_type::assign(__p[__newsz], value_type());
| ^
/usr/include/c++/v1/string:2134:5: note: in instantiation of member function 'std::basic_string<unsigned int>::__null_terminate_at' requested here
2134 | __null_terminate_at(std::__to_address(__get_pointer()), __pos);
| ^
/usr/include/c++/v1/string:3304:5: note: in instantiation of member function 'std::basic_string<unsigned int>::__erase_to_end' requested here
3304 | __erase_to_end(__n);
| ^
/usr/include/c++/v1/string:1303:84: note: in instantiation of member function 'std::basic_string<unsigned int>::resize' requested here
1303 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 void resize(size_type __n) { resize(__n, value_type()); }
| ^
../dlib-19.24/dlib/all/../bigint/../serialize.h:2011:14: note: in instantiation of member function 'std::basic_string<unsigned int>::resize' requested here
2011 | item.resize(size);
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2825:29: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2825 | ? (__fits_in_sso(traits_type::length(__s)) ? __assign_short(__s, traits_type::length(__s))
| ^
../dlib-19.24/dlib/all/../unicode/unicode.cpp:54:14: note: in instantiation of member function 'std::basic_string<unsigned int>::assign' requested here
54 | dest.assign((const unichar *)(src));
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2825:77: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2825 | ? (__fits_in_sso(traits_type::length(__s)) ? __assign_short(__s, traits_type::length(__s))
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2826:80: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2826 | : __assign_external(__s, traits_type::length(__s)))
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2208:5: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2208 | traits_type::move(std::__to_address(__p), __s, __n);
| ^
/usr/include/c++/v1/string:2825:57: note: in instantiation of member function 'std::basic_string<unsigned int>::__assign_short' requested here
2825 | ? (__fits_in_sso(traits_type::length(__s)) ? __assign_short(__s, traits_type::length(__s))
| ^
../dlib-19.24/dlib/all/../unicode/unicode.cpp:54:14: note: in instantiation of member function 'std::basic_string<unsigned int>::assign' requested here
54 | dest.assign((const unichar *)(src));
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2209:5: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2209 | traits_type::assign(__p[__n], value_type());
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:11:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.cpp:6:
In file included from ../dlib-19.24/dlib/all/../base64/base64_kernel_1.h:6:
In file included from ../dlib-19.24/dlib/all/../base64/../algs.h:97:
/usr/include/c++/v1/string:2817:33: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
2817 | return __assign_external(__s, traits_type::length(__s));
| ^
/usr/include/c++/v1/string:2827:14: note: in instantiation of member function 'std::basic_string<unsigned int>::__assign_external' requested here
2827 | : __assign_external(__s);
| ^
../dlib-19.24/dlib/all/../unicode/unicode.cpp:54:14: note: in instantiation of member function 'std::basic_string<unsigned int>::assign' requested here
54 | dest.assign((const unichar *)(src));
| ^
/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
| ^
In file included from ../dlib-19.24/dlib/all/source.cpp:82:
In file included from ../dlib-19.24/dlib/all/../cuda/cpu_dlib.cpp:8:
In file included from ../dlib-19.24/dlib/all/../cuda/cpu_dlib.h:9:
In file included from ../dlib-19.24/dlib/all/../cuda/tensor.h:8:
In file included from ../dlib-19.24/dlib/all/../cuda/../matrix.h:6:
../dlib-19.24/dlib/all/../cuda/../matrix/matrix.h:1153:47: warning: division by zero is undefined [-Wdivision-by-zero]
1153 | data.set_size(NR, l.size()/NR);
| ^~~
../dlib-19.24/dlib/all/../svm/auto.cpp:78:13: note: in instantiation of member function 'dlib::matrix<double, 0, 1>::matrix' requested here
78 | {1e-5, 1e-5, 1e-5}, // lower bound constraints on gamma, c1, and c2, respectively
| ^
1 warning and 17 errors generated.
gmake[4]: *** [Makefile:2588: ../dlib-19.24/dlib/all/libRNA_concentrations_la-source.lo] Error 1
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA'
gmake[3]: *** [Makefile:3218: all-recursive] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA'
gmake[2]: *** [Makefile:566: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src'
gmake[1]: *** [Makefile:746: all-recursive] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0'
gmake: *** [Makefile:627: all] Error 2
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/viennarna