[package - head-armv7-default][biology/cufflinks] Failed for cufflinks-2.2.1.83 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Wed May 29 21:50:11 UTC 2019
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 at FreeBSD.org
Last committer: yuri at FreeBSD.org
Ident: $FreeBSD: head/biology/cufflinks/Makefile 502661 2019-05-25 22:28:12Z yuri $
Log URL: http://beefy16.nyi.freebsd.org/data/head-armv7-default/p502843_s348318/logs/cufflinks-2.2.1.83.log
Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p502843_s348318
Log:
=>> Building biology/cufflinks
build started at Wed May 29 21:48:57 UTC 2019
port directory: /usr/ports/biology/cufflinks
package name: cufflinks-2.2.1.83
building for: FreeBSD head-armv7-default-job-24 13.0-CURRENT FreeBSD 13.0-CURRENT 1300029 arm
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/cufflinks/Makefile 502661 2019-05-25 22:28:12Z yuri $
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!!! Jail is newer than host. (Jail: 1300029, Host: 1300018) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
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=======================<phase: check-sanity >============================
===> License BSL accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> cufflinks-2.2.1.83 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.5_5.txz
[head-armv7-default-job-24] Installing pkg-1.10.5_5...
[head-armv7-default-job-24] Extracting pkg-1.10.5_5: .......... done
===> cufflinks-2.2.1.83 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of cufflinks-2.2.1.83
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSL accepted by the user
<snip>
src/Makefile.am: installing 'build-aux/depcomp'
configure: loading site script /usr/ports/Templates/config.site
checking for a BSD-compatible install... /usr/bin/install -c
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checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether gmake sets $(MAKE)... yes
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checking for gawk... (cached) /usr/bin/awk
checking whether the C++ compiler works... yes
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checking for boostlib >= 1.47.0... yes
checking for htslib or bamlib... yes
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checking for exit in -lboost_system... yes
checking for exit in -lboost_system... (cached) yes
checking whether the Boost::Serialization library is available... yes
checking for exit in -lboost_serialization... yes
checking for exit in -lboost_serialization... (cached) yes
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checking for exit in -lboost_filesystem... yes
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checking for exit in -lboost_system... (cached) yes
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checking for grep that handles long lines and -e... (cached) /usr/bin/grep
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checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking for zlib.h... (cached) yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
./configure: AX_EIGEN: not found
checking for stdlib.h... (cached) yes
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checking dependency style of /nxb-bin/usr/bin/cc... (cached) gcc3
checking dependency style of /nxb-bin/usr/bin/c++... (cached) gcc3
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
-- cufflinks 2.2.2 Configuration Results --
C++ compiler: /nxb-bin/usr/bin/c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -fstack-protector-strong -L/usr/lib
GCC version: FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0)
Host System type: armv7-portbld-freebsd13.0
Install prefix: /usr/local
Install eprefix: ${prefix}
See config.h for further configuration information.
Email <cole at cs.umd.edu> with questions and bug reports.
===========================================================================
=======================<phase: build >============================
===> Building for cufflinks-2.2.1.83
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050'
gmake all-recursive
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050'
Making all in src
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050/src'
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT cufflinks.o -MD -MP -MF .deps/cufflinks.Tpo -c -o cufflinks.o cufflinks.cpp
In file included from cufflinks.cpp:12:
In file included from /usr/include/c++/v1/string:505:
In file included from /usr/include/c++/v1/string_view:176:
In file included from /usr/include/c++/v1/__string:57:
In file included from /usr/include/c++/v1/algorithm:644:
In file included from /usr/include/c++/v1/memory:654:
/usr/include/c++/v1/typeinfo:189:14: error: cast from pointer to smaller type 'size_t' (aka 'unsigned int') loses information
{ return reinterpret_cast<size_t>(__type_name); }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from cufflinks.cpp:12:
In file included from /usr/include/c++/v1/string:505:
In file included from /usr/include/c++/v1/string_view:176:
In file included from /usr/include/c++/v1/__string:57:
In file included from /usr/include/c++/v1/algorithm:644:
In file included from /usr/include/c++/v1/memory:657:
/usr/include/c++/v1/new:172:66: error: 'operator new' takes type size_t ('unsigned long') as first parameter
_LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_OVERRIDABLE_FUNC_VIS void* operator new(std::size_t __sz) _THROW_BAD_ALLOC;
^
/usr/include/c++/v1/new:173:66: error: 'operator new' takes type size_t ('unsigned long') as first parameter
_LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_OVERRIDABLE_FUNC_VIS void* operator new(std::size_t __sz, const std::nothrow_t&) _NOEXCEPT _NOALIAS;
^
/usr/include/c++/v1/new:180:66: error: 'operator new[]' takes type size_t ('unsigned long') as first parameter
_LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_OVERRIDABLE_FUNC_VIS void* operator new[](std::size_t __sz) _THROW_BAD_ALLOC;
^
/usr/include/c++/v1/new:181:66: error: 'operator new[]' takes type size_t ('unsigned long') as first parameter
_LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_OVERRIDABLE_FUNC_VIS void* operator new[](std::size_t __sz, const std::nothrow_t&) _NOEXCEPT _NOALIAS;
^
/usr/include/c++/v1/new:189:66: error: 'operator new' takes type size_t ('unsigned long') as first parameter
_LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_OVERRIDABLE_FUNC_VIS void* operator new(std::size_t __sz, std::align_val_t) _THROW_BAD_ALLOC;
^
/usr/include/c++/v1/new:190:66: error: 'operator new' takes type size_t ('unsigned long') as first parameter
_LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_OVERRIDABLE_FUNC_VIS void* operator new(std::size_t __sz, std::align_val_t, const std::nothrow_t&) _NOEXCEPT _NOALIAS;
^
/usr/include/c++/v1/new:197:66: error: 'operator new[]' takes type size_t ('unsigned long') as first parameter
_LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_OVERRIDABLE_FUNC_VIS void* operator new[](std::size_t __sz, std::align_val_t) _THROW_BAD_ALLOC;
^
/usr/include/c++/v1/new:198:66: error: 'operator new[]' takes type size_t ('unsigned long') as first parameter
_LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_OVERRIDABLE_FUNC_VIS void* operator new[](std::size_t __sz, std::align_val_t, const std::nothrow_t&) _NOEXCEPT _NOALIAS;
^
/usr/include/c++/v1/new:206:70: error: 'operator new' takes type size_t ('unsigned long') as first parameter
_LIBCPP_NODISCARD_AFTER_CXX17 inline _LIBCPP_INLINE_VISIBILITY void* operator new (std::size_t, void* __p) _NOEXCEPT {return __p;}
^
/usr/include/c++/v1/new:207:70: error: 'operator new[]' takes type size_t ('unsigned long') as first parameter
_LIBCPP_NODISCARD_AFTER_CXX17 inline _LIBCPP_INLINE_VISIBILITY void* operator new[](std::size_t, void* __p) _NOEXCEPT {return __p;}
^
In file included from cufflinks.cpp:12:
In file included from /usr/include/c++/v1/string:505:
In file included from /usr/include/c++/v1/string_view:176:
In file included from /usr/include/c++/v1/__string:57:
In file included from /usr/include/c++/v1/algorithm:644:
/usr/include/c++/v1/memory:2052:73: error: too many arguments to function call, expected 1, have 2
__r.first = static_cast<_Tp*>(::operator new(__n * sizeof(_Tp), nothrow));
~~~~~~~~~~~~~~ ^~~~~~~
note: 'operator new' declared here
In file included from cufflinks.cpp:12:
In file included from /usr/include/c++/v1/string:505:
/usr/include/c++/v1/string_view:797:63: error: invalid literal operator parameter type 'size_t' (aka 'unsigned int'), did you mean 'unsigned long'?
basic_string_view<char> operator "" sv(const char *__str, size_t __len) _NOEXCEPT
^~~~~~~~~~~~
/usr/include/c++/v1/string_view:803:69: error: invalid literal operator parameter type 'size_t' (aka 'unsigned int'), did you mean 'unsigned long'?
basic_string_view<wchar_t> operator "" sv(const wchar_t *__str, size_t __len) _NOEXCEPT
^~~~~~~~~~~~
/usr/include/c++/v1/string_view:817:71: error: invalid literal operator parameter type 'size_t' (aka 'unsigned int'), did you mean 'unsigned long'?
basic_string_view<char16_t> operator "" sv(const char16_t *__str, size_t __len) _NOEXCEPT
^~~~~~~~~~~~
/usr/include/c++/v1/string_view:823:71: error: invalid literal operator parameter type 'size_t' (aka 'unsigned int'), did you mean 'unsigned long'?
basic_string_view<char32_t> operator "" sv(const char32_t *__str, size_t __len) _NOEXCEPT
^~~~~~~~~~~~
In file included from cufflinks.cpp:12:
/usr/include/c++/v1/string:4342:58: error: invalid literal operator parameter type 'size_t' (aka 'unsigned int'), did you mean 'unsigned long'?
basic_string<char> operator "" s( const char *__str, size_t __len )
^~~~~~~~~~~~
/usr/include/c++/v1/string:4348:64: error: invalid literal operator parameter type 'size_t' (aka 'unsigned int'), did you mean 'unsigned long'?
basic_string<wchar_t> operator "" s( const wchar_t *__str, size_t __len )
^~~~~~~~~~~~
/usr/include/c++/v1/string:4362:66: error: invalid literal operator parameter type 'size_t' (aka 'unsigned int'), did you mean 'unsigned long'?
basic_string<char16_t> operator "" s( const char16_t *__str, size_t __len )
^~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
gmake[3]: *** [Makefile:1672: cufflinks.o] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050/src'
gmake[2]: *** [Makefile:400: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050'
gmake[1]: *** [Makefile:341: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/cufflinks
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