Package Details: blast+ 2.7.1-2

Git Clone URL: https://aur.archlinux.org/blast+.git (read-only)
Package Base: blast+
Description: BLAST tool suite from NCBI (blastn, blastp, blastx, psiblast, etc)
Upstream URL: http://blast.ncbi.nlm.nih.gov/
Licenses: custom
Conflicts: blast, blast+-bin, cddlib, ncbi-blast, proj
Provides: blast, blast+-binncbi-blast
Replaces: ncbi-blast
Submitter: wookietreiber
Maintainer: nstickney
Last Packager: nstickney
Votes: 4
Popularity: 0.122252
First Submitted: 2015-07-07 11:11
Last Updated: 2018-04-03 16:03

Latest Comments

nstickney commented on 2018-04-03 16:02

@kieto @anadon @wookietreiber I've updated based on @kieto's suggestion and it compiles for me, but as I said, I'm no longer using blast+ in my research so if anyone wants to take over/co-maintain/whatever, let me know!

kieto commented on 2018-04-02 20:00

I was getting compilation errors regarding Boost and so on, and as suggested by the compiler, I edited the PKGBUILD and added the flags --without-boost and --without-bdb, and I got a successful compilation (at first I only used the flag --without-boost, but I was still getting compilation errors). The modified source PKGBUILD, prepare() section, looks like this:

prepare() {
    cd $srcdir/ncbi-blast-$pkgver+-src/c++
    ./configure \
        --prefix=/usr \
        --with-dll \
        --with-mt \
        --without-gnutls \
        --without-boost \
        --without-bdb
}

https://pastebin.com/GXBTLMYH

nstickney commented on 2018-03-08 17:17

@anadon I'm not going to be able to get to this for a couple of months due to other concerns (and I'm no longer using the blast+ tools in my research). If you would like to take over as manager for the package, I'll be glad to orphan it!

anadon commented on 2018-03-08 15:36

@nstickney NCBI is developing on a 2.7.2 branch which does work with Boost 1.66 and should be released soon. You might consider basing this off of their SVN repo here: https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/c++

If you drop an email to NCBI, turns out their devs are really friendly and helpful.

nstickney commented on 2018-03-06 04:00

@anadon I'm not able to download the sources to recheck, currently (seems the site is down, or something?). Were you able to diagnose/overcome the issue?

anadon commented on 2018-02-28 19:33

Looks like there is some bug when compiling:

(sanely formatted: https://pastebin.com/C9d90Bfx)

/usr/bin/g++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -march=native -Ofast -pipe --param=ssp-buffer-size=4 -fPIC -O -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_FORTIFY_SOURCE=2 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/ReleaseMT/inc -I/tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/include /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_messages.cpp -o teamcity_messages.o /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In constructor ‘ncbi::CNcbiTestApplication::CNcbiTestApplication()’: /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:925:39: error: invalid new-expression of abstract class type ‘ncbi::CNcbiBoostLogger’ m_Logger = new CNcbiBoostLogger(); ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:224:7: note: because the following virtual functions are pure within ‘ncbi::CNcbiBoostLogger’: class CNcbiBoostLogger : public TBoostLogFormatter ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/test/output/compiler_log_formatter.hpp:17:0, from /usr/include/boost/test/impl/compiler_log_formatter.ipp:19, from /usr/include/boost/test/included/unit_test.hpp:18, from /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:70: /usr/include/boost/test/unit_test_log_formatter.hpp:267:25: note: virtual void boost::unit_test::unit_test_log_formatter::log_entry_context(std::ostream&, boost::unit_test::log_level, boost::unit_test::const_string) virtual void log_entry_context( std::ostream& os, log_level l, const_string value ) = 0; ^~~~~~~~~~~~~~~~~ /usr/include/boost/test/unit_test_log_formatter.hpp:274:25: note: virtual void boost::unit_test::unit_test_log_formatter::entry_context_finish(std::ostream&, boost::unit_test::log_level) virtual void entry_context_finish( std::ostream& os, log_level l ) = 0; ^~~~~~~~~~~~~~~~~~~~ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In member function ‘void ncbi::CNcbiTestApplication::SetTestDisabled(boost::unit_test::test_unit)’: /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:116:37: error: ‘RUN_FILTERS’ is not a member of ‘boost::unit_test::runtime_config’ RTCFG(std::vector<std::string>, RUN_FILTERS, test_to_run) ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’ but::runtime_config::get<type>(but::runtime_config::new_name) ^~~~~~~~ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:997:9: note: in expansion of macro ‘CONFIGURED_FILTERS’ if (CONFIGURED_FILTERS.empty()) { ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In member function ‘void ncbi::CNcbiTestApplication::x_SetupBoostReporters()’: /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:1665:59: error: ‘REPORT_FORMAT’ is not a member of ‘boost::unit_test::runtime_config’ but::output_format format = RTCFG(but::output_format, REPORT_FORMAT, ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’ but::runtime_config::get<type>(but::runtime_config::new_name) ^~~~~~~~ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:1693:57: error: ‘LOG_FORMAT’ is not a member of ‘boost::unit_test::runtime_config’ m_Logger->SetOutputFormat(RTCFG(but::output_format, LOG_FORMAT, ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’ but::runtime_config::get<type>(but::runtime_config::new_name) ^~~~~~~~ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In member function ‘boost::unit_test::test_suite</type></type></type></std::string> ncbi::CNcbiTestApplication::InitTestFramework(int, char)’: /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:116:37: error: ‘RUN_FILTERS’ is not a member of ‘boost::unit_test::runtime_config’ RTCFG(std::vector<std::string>, RUN_FILTERS, test_to_run) ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’ but::runtime_config::get<type>(but::runtime_config::new_name) ^~~~~~~~ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:1815:19: note: in expansion of macro ‘CONFIGURED_FILTERS’ && (!CONFIGURED_FILTERS.empty() || x_ReadConfiguration())) ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In member function ‘virtual void ncbi::CNcbiBoostLogger::log_entry_context(std::ostream&, boost::unit_test::const_string)’: /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2130:43: error: no matching function for call to ‘boost::unit_test::unit_test_log_formatter::log_entry_context(std::ostream&, boost::unit_test::const_string&)’ m_Upper->log_entry_context(ostr, value); ^ In file included from /usr/include/boost/test/output/compiler_log_formatter.hpp:17:0, from /usr/include/boost/test/impl/compiler_log_formatter.ipp:19, from /usr/include/boost/test/included/unit_test.hpp:18, from /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:70: /usr/include/boost/test/unit_test_log_formatter.hpp:267:25: note: candidate: virtual void boost::unit_test::unit_test_log_formatter::log_entry_context(std::ostream&, boost::unit_test::log_level, boost::unit_test::const_string) virtual void log_entry_context( std::ostream& os, log_level l, const_string value ) = 0; ^~~~~~~~~~~~~~~~~ /usr/include/boost/test/unit_test_log_formatter.hpp:267:25: note: candidate expects 3 arguments, 2 provided /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In member function ‘virtual void ncbi::CNcbiBoostLogger::entry_context_finish(std::ostream&)’: /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2135:39: error: no matching function for call to ‘boost::unit_test::unit_test_log_formatter::entry_context_finish(std::ostream&)’ m_Upper->entry_context_finish(ostr); ^ In file included from /usr/include/boost/test/output/compiler_log_formatter.hpp:17:0, from /usr/include/boost/test/impl/compiler_log_formatter.ipp:19, from /usr/include/boost/test/included/unit_test.hpp:18, from /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:70: /usr/include/boost/test/unit_test_log_formatter.hpp:274:25: note: candidate: virtual void boost::unit_test::unit_test_log_formatter::entry_context_finish(std::ostream&, boost::unit_test::log_level) virtual void entry_context_finish( std::ostream& os, log_level l ) = 0; ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/test/unit_test_log_formatter.hpp:274:25: note: candidate expects 2 arguments, 1 provided In file included from /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2227:0: /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_boost.cpp: In constructor ‘jetbrains::teamcity::TeamcityFormatterRegistrar::TeamcityFormatterRegistrar()’: /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_boost.cpp:92:89: error: invalid new-expression of abstract class type ‘jetbrains::teamcity::TeamcityBoostLogFormatter’ boost::unit_test::unit_test_log.set_formatter(new TeamcityBoostLogFormatter()); ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_boost.cpp:44:7: note: because the following virtual functions are pure within ‘jetbrains::teamcity::TeamcityBoostLogFormatter’: class TeamcityBoostLogFormatter: public boost::unit_test::unit_test_log_formatter { ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/test/output/compiler_log_formatter.hpp:17:0, from /usr/include/boost/test/impl/compiler_log_formatter.ipp:19, from /usr/include/boost/test/included/unit_test.hpp:18, from /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:70: /usr/include/boost/test/unit_test_log_formatter.hpp:267:25: note: virtual void boost::unit_test::unit_test_log_formatter::log_entry_context(std::ostream&, boost::unit_test::log_level, boost::unit_test::const_string) virtual void log_entry_context( std::ostream& os, log_level l, const_string value ) = 0; ^~~~~~~~~~~~~~~~~ /usr/include/boost/test/unit_test_log_formatter.hpp:274:25: note: virtual void boost::unit_test::unit_test_log_formatter::entry_context_finish(std::ostream&, boost::unit_test::log_level) virtual void entry_context_finish( std::ostream& os, log_level l ) = 0; ^~~~~~~~~~~~~~~~~~~~ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_boost.cpp:94:40: error: ‘LOG_LEVEL’ is not a member of ‘boost::unit_test::runtime_config’ (RTCFG(but::log_level, LOG_LEVEL, log_level)); ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’ but::runtime_config::get<type>(but::runtime_config::new_name) ^~~~~~~~ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In function ‘int main(int, char</type></type></std::string>)’: /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2266:25: error: ‘WAIT_FOR_DEBUGGER’ is not a member of ‘boost::unit_test::runtime_config’ if( RTCFG(bool, WAIT_FOR_DEBUGGER, wait_for_debugger) ) { ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’ but::runtime_config::get<type>(but::runtime_config::new_name) ^~~~~~~~ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2275:56: error: ‘LIST_CONTENT’ is not a member of ‘boost::unit_test::runtime_config’ output_format list_cont = RTCFG(output_format, LIST_CONTENT, ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’ but::runtime_config::get<type>(but::runtime_config::new_name) ^~~~~~~~ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2292:25: error: ‘LIST_LABELS’ is not a member of ‘boost::unit_test::runtime_config’ if( RTCFG(bool, LIST_LABELS, list_labels) ) { ^ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’ but::runtime_config::get<type>(but::runtime_config::new_name) ^~~~~~~~ /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2319:56: error: ‘RESULT_CODE’ is not a member of ‘boost::unit_test::runtime_config’ runtime_config::get<bool>( runtime_config::RESULT_CODE )</bool></type></type></type>

sguyader commented on 2017-12-04 11:28

@wookietreiber trying editing the PKGBUILD script, and add --disable-boost at the configuration command.

wookietreiber commented on 2016-06-26 08:51

Cannot compile the new version 2.4.0 because it fails to compile with the following error:

fatal error: boost/test/unit_test_suite_impl.hpp: No such file or directory
#include <boost/test/unit_test_suite_impl.hpp>

I don't know what to make of this, because this file does not exist within boost. There is a /usr/include/boost/test/unit_test_suite.hpp but this doesn't help much. Anyone got any ideas?

wookietreiber commented on 2016-04-06 13:06

@masonmlai it would also help to get your compilation logs / errors in some gist / pastebin.

wookietreiber commented on 2016-04-06 13:05

I just tried to reproduce and couldn't. I have boost-libs installed - just not boost:

$ pacman -Q | grep boost
boost-libs 1.60.0-2

Compilation succeeded without problems. @masonmlai do you have package boost installed additionally to boost-libs?

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