Opened 7 years ago

Closed 3 years ago

#43306 closed defect (fixed)

clustalx @2.1: error: implicit instantiation of undefined template 'std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >'

Reported by: pst@… Owned by: nerdling (Jeremy Lavergne)
Priority: Normal Milestone:
Component: ports Version: 2.2.1
Keywords: Cc:
Port: clustalx

Description (last modified by ryandesign (Ryan Schmidt))

I have a fresh install of macports. I did "sudo port install clustalx", got:

Error: org.macports.build for port clustalx returned: command execution failed
Please see the log file for port clustalx for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_clustalx/clustalx/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port clustalx failed

Log attached.

Attachments (1)

main.log (236.7 KB) - added by pst@… 7 years ago.
Build error log for clustalx

Download all attachments as: .zip

Change History (5)

Changed 7 years ago by pst@…

Attachment: main.log added

Build error log for clustalx

comment:1 Changed 7 years ago by ryandesign (Ryan Schmidt)

Description: modified (diff)
Owner: changed from macports-tickets@… to snc@…
Port: clustalx added
Summary: clustalx 2.1, build errorclustalx @2.1: error: implicit instantiation of undefined template 'std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >'

The first error in the log seems to be:

:info:build In file included from clustalW/general/VectorOutOfRange.cpp:9:
:info:build clustalW/general/VectorOutOfRange.h:23:21: error: implicit instantiation of undefined template 'std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >'
:info:build         std::string _name;
:info:build                     ^
:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iosfwd:188:33: note: template is declared here
:info:build     class _LIBCPP_TYPE_VIS_ONLY basic_string;
:info:build                                 ^

comment:2 Changed 6 years ago by nerdling (Jeremy Lavergne)

Status: newassigned

comment:3 Changed 6 years ago by nerdling (Jeremy Lavergne)

After blacklisting clang/llvm, using MacPorts' apple-gcc-4.2 compiler got me to:

make: *** [AlignmentParameters.o] Segmentation fault: 11

comment:4 Changed 3 years ago by ryandesign (Ryan Schmidt)

Resolution: fixed
Status: assignedclosed

In 346a60ff1acc996b7830b877763a114bf09ef934/macports-ports (master):

clustalx: Fix build failures

Fix build failures due to lack of <string> include and lack of path to
Qt frameworks.

Closes: #43306

Include qmake portgroup to simplify the portfile and to use the right
-arch flags, which also enables the universal variant. This also fixes
qt4-mac to be a library dependency, which requires increasing the
revision.

See: #39424

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