papara problems on a Mac

[cmc...@uw.edu]

Hello, thanks for your work on raxml and papara.

I'm having a problem with papara on the mac. I tried the precompiled binary on a High Sierra system, and got the following:

$ papara -t RAxML_bestTree.rpsD_AA -s rpsD_AA_aln.phymlAln.reduced -q rpsD_AA_translation_stops_removed.fasta -n rpsD_AA_artificialMG -j 8 -a -f

papara called as:

papara -t RAxML_bestTree.rpsD_AA -s rpsD_AA_aln.phymlAln.reduced -q rpsD_AA_translation_stops_removed.fasta -n rpsD_AA_artificialMG -j 8 -a -f  

Illegal instruction: 4

I'm sure my input files and command are correct because I have access to a linux machine with papara installed, and the command works as expected. Therefore, I tried to compile my own papara binary. I followed the instructions and installed boost with homebrew, but I get the following when I try to compile version 2.5:

$ sh build_papara2.sh
papara.cpp:22:10: fatal error: 'boost/bind.hpp' file not found
#include <boost/bind.hpp>
         ^~~~~~~~~~~~~~~~
1 error generated.
In file included from pvec.cpp:21:
./pvec.h:24:10: fatal error: 'boost/numeric/ublas/matrix.hpp' file not found
#include <boost/numeric/ublas/matrix.hpp>
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
In file included from papara2_main.cpp:25:
./papara.h:38:10: fatal error: 'boost/io/ios_state.hpp' file not found
#include <boost/io/ios_state.hpp>
         ^~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
In file included from blast_partassign.cpp:13:
./papara.h:38:10: fatal error: 'boost/io/ios_state.hpp' file not found
#include <boost/io/ios_state.hpp>
         ^~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
In file included from ivy_mike/src/tree_parser.cpp:23:
ivy_mike/src/ivymike/tree_parser.h:38:10: fatal error: 'boost/intrusive/slist.hpp' file not found
#include <boost/intrusive/slist.hpp>
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
ublasJama-1.0.2.3/EigenvalueDecomposition.cpp:20:10: fatal error: 'boost/math/special_functions/hypot.hpp' file not found
#include <boost/math/special_functions/hypot.hpp>

I do have xcode and xcode command line tools installed. Any help or tips would be much appreciated. 

best,

Cedar

[Lucas Czech]

Hi Cedar,

it has been a while since I built the Mac binary for PaPaRa, so I do not remember what exactly I did to get it to work. The Mac version was different though, and the hardware is probably different. The error "illegal instruction" hints that some CPU feature that was available when I compiled it is not available on your Mac. How old is your machine?

In order to compile on your own, here are two ideas you can try:

• Add -I<boost dir> to the command line for the compiler/linker, where the boost dir is the subdirectory of your boost installation called "boost", which contains a lot of ".hpp" files.
• Add a shortcut/symlink to this directory to your PaPaRa dir, and call it "boost". This should work the same way and help the compiler to find the files.

Let me know if either of those works.

Best
Lucas

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[Cedar McKay]

Thanks for your response. I followed your suggestion on two different macs running high sierra. If I use boost 1.68, I get errors about missing ‘unordered_set.hpp’. I searched the boost directory, and there are four files named unordered_set.hpp’ in various places, but there is no tr1 subdirectory at all.


> $ sh build_papara2.sh
> In file included from papara.cpp:30:
> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> ivy_mike/src/ivymike/tree_traversal_utils.h:30:10: fatal error: 'boost/tr1/unordered_set.hpp' file not found
> #include <boost/tr1/unordered_set.hpp>
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

> 1 error generated.
> In file included from pvec.cpp:21:

> In file included from ./pvec.h:41:
> ivy_mike/src/ivymike/tree_traversal_utils.h:30:10: fatal error: 'boost/tr1/unordered_set.hpp' file not found
> #include <boost/tr1/unordered_set.hpp>
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

> 1 error generated.
> In file included from papara2_main.cpp:25:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> ivy_mike/src/ivymike/tree_traversal_utils.h:30:10: fatal error: 'boost/tr1/unordered_set.hpp' file not found
> #include <boost/tr1/unordered_set.hpp>
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

> 1 error generated.
> In file included from blast_partassign.cpp:13:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> ivy_mike/src/ivymike/tree_traversal_utils.h:30:10: fatal error: 'boost/tr1/unordered_set.hpp' file not found
> #include <boost/tr1/unordered_set.hpp>
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 1 error generated.






If I use boost 1.41 (this is the version with which I’d previously managed to compile papara) I get the many error listed below. Any help is much appreciated.





> $ sh build_papara2.sh
> In file included from papara.cpp:30:
> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:34:33: error: reference to 'pair' is ambiguous
> std::size_t hash_value(std::pair<A, B> const&);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/utility:312:29: note: candidate found by name lookup is
> 'std::__1::pair'
> struct _LIBCPP_TEMPLATE_VIS pair
> ^
> ./boost/detail/container_fwd.hpp:90:42: note: candidate found by name lookup is 'std::pair'
> template <class T1, class T2> struct pair;
> ^
> In file included from papara.cpp:30:
> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:34:33: error: no template named 'pair' in namespace 'std'
> std::size_t hash_value(std::pair<A, B> const&);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:34:44: error: expected ')'
> std::size_t hash_value(std::pair<A, B> const&);
> ^
> ./boost/functional/hash/extensions.hpp:34:27: note: to match this '('
> std::size_t hash_value(std::pair<A, B> const&);
> ^
> ./boost/functional/hash/extensions.hpp:36:33: error: reference to 'vector' is ambiguous
> std::size_t hash_value(std::vector<T, A> const&);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1407:74: note: candidate found by name lookup is
> 'std::__1::vector'
> template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
> ^
> ./boost/detail/container_fwd.hpp:80:47: note: candidate found by name lookup is 'std::vector'
> template <class T, class Allocator> class vector;
> ^
> In file included from papara.cpp:30:
> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:36:33: error: no template named 'vector' in namespace 'std'
> std::size_t hash_value(std::vector<T, A> const&);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:36:46: error: expected ')'
> std::size_t hash_value(std::vector<T, A> const&);
> ^
> ./boost/functional/hash/extensions.hpp:36:27: note: to match this '('
> std::size_t hash_value(std::vector<T, A> const&);
> ^
> ./boost/functional/hash/extensions.hpp:40:33: error: reference to 'deque' is ambiguous
> std::size_t hash_value(std::deque<T, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/deque:1187:28: note: candidate found by name lookup is
> 'std::__1::deque'
> class _LIBCPP_TEMPLATE_VIS deque
> ^
> ./boost/detail/container_fwd.hpp:76:47: note: candidate found by name lookup is 'std::deque'
> template <class T, class Allocator> class deque;
> ^
> In file included from papara.cpp:30:
> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:40:33: error: no template named 'deque' in namespace 'std'
> std::size_t hash_value(std::deque<T, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:40:45: error: expected ')'
> std::size_t hash_value(std::deque<T, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:40:27: note: to match this '('
> std::size_t hash_value(std::deque<T, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:42:33: error: reference to 'set' is ambiguous
> std::size_t hash_value(std::set<K, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/set:400:28: note: candidate found by name lookup is
> 'std::__1::set'
> class _LIBCPP_TEMPLATE_VIS set
> ^
> ./boost/detail/container_fwd.hpp:84:64: note: candidate found by name lookup is 'std::set'
> template <class Key, class Compare, class Allocator> class set;
> ^
> In file included from papara.cpp:30:
> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:42:33: error: no template named 'set' in namespace 'std'
> std::size_t hash_value(std::set<K, C, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:42:46: error: expected ')'
> std::size_t hash_value(std::set<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:42:27: note: to match this '('
> std::size_t hash_value(std::set<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:44:33: error: reference to 'multiset' is ambiguous
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/set:809:28: note: candidate found by name lookup is
> 'std::__1::multiset'
> class _LIBCPP_TEMPLATE_VIS multiset
> ^
> ./boost/detail/container_fwd.hpp:85:64: note: candidate found by name lookup is 'std::multiset'
> template <class Key, class Compare, class Allocator> class multiset;
> ^
> In file included from papara.cpp:30:
> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:44:33: error: no template named 'multiset' in namespace 'std'
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:44:51: error: expected ')'
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:44:27: note: to match this '('
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:46:33: error: reference to 'map' is ambiguous
> std::size_t hash_value(std::map<K, T, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/map:805:28: note: candidate found by name lookup is
> 'std::__1::map'
> class _LIBCPP_TEMPLATE_VIS map
> ^
> ./boost/detail/container_fwd.hpp:81:73: note: candidate found by name lookup is 'std::map'
> template <class Key, class T, class Compare, class Allocator> class map;
> ^
> In file included from papara.cpp:30:
> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:46:33: error: no template named 'map' in namespace 'std'
> std::size_t hash_value(std::map<K, T, C, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:46:49: error: expected ')'
> std::size_t hash_value(std::map<K, T, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:46:27: note: to match this '('
> std::size_t hash_value(std::map<K, T, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:48:33: error: reference to 'multimap' is ambiguous
> std::size_t hash_value(std::multimap<K, T, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/map:1461:28: note: candidate found by name lookup is
> 'std::__1::multimap'
> class _LIBCPP_TEMPLATE_VIS multimap
> ^
> ./boost/detail/container_fwd.hpp:83:11: note: candidate found by name lookup is 'std::multimap'
> class multimap;
> ^
> fatal error: too many errors emitted, stopping now [-ferror-limit=]
> 20 errors generated.

> In file included from pvec.cpp:21:

> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:34:33: error: reference to 'pair' is ambiguous
> std::size_t hash_value(std::pair<A, B> const&);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/utility:312:29: note: candidate found by name lookup is
> 'std::__1::pair'
> struct _LIBCPP_TEMPLATE_VIS pair
> ^
> ./boost/detail/container_fwd.hpp:90:42: note: candidate found by name lookup is 'std::pair'
> template <class T1, class T2> struct pair;
> ^

> In file included from pvec.cpp:21:

> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:34:33: error: no template named 'pair' in namespace 'std'
> std::size_t hash_value(std::pair<A, B> const&);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:34:44: error: expected ')'
> std::size_t hash_value(std::pair<A, B> const&);
> ^
> ./boost/functional/hash/extensions.hpp:34:27: note: to match this '('
> std::size_t hash_value(std::pair<A, B> const&);
> ^
> ./boost/functional/hash/extensions.hpp:36:33: error: reference to 'vector' is ambiguous
> std::size_t hash_value(std::vector<T, A> const&);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/vector:447:28: note: candidate found by name lookup is
> 'std::__1::vector'
> class _LIBCPP_TEMPLATE_VIS vector
> ^
> ./boost/detail/container_fwd.hpp:80:47: note: candidate found by name lookup is 'std::vector'
> template <class T, class Allocator> class vector;
> ^

> In file included from pvec.cpp:21:

> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:36:33: error: no template named 'vector' in namespace 'std'
> std::size_t hash_value(std::vector<T, A> const&);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:36:46: error: expected ')'
> std::size_t hash_value(std::vector<T, A> const&);
> ^
> ./boost/functional/hash/extensions.hpp:36:27: note: to match this '('
> std::size_t hash_value(std::vector<T, A> const&);
> ^
> ./boost/functional/hash/extensions.hpp:42:33: error: reference to 'set' is ambiguous
> std::size_t hash_value(std::set<K, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/set:400:28: note: candidate found by name lookup is
> 'std::__1::set'
> class _LIBCPP_TEMPLATE_VIS set
> ^
> ./boost/detail/container_fwd.hpp:84:64: note: candidate found by name lookup is 'std::set'
> template <class Key, class Compare, class Allocator> class set;
> ^

> In file included from pvec.cpp:21:

> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:42:33: error: no template named 'set' in namespace 'std'
> std::size_t hash_value(std::set<K, C, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:42:46: error: expected ')'
> std::size_t hash_value(std::set<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:42:27: note: to match this '('
> std::size_t hash_value(std::set<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:44:33: error: reference to 'multiset' is ambiguous
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/set:809:28: note: candidate found by name lookup is
> 'std::__1::multiset'
> class _LIBCPP_TEMPLATE_VIS multiset
> ^
> ./boost/detail/container_fwd.hpp:85:64: note: candidate found by name lookup is 'std::multiset'
> template <class Key, class Compare, class Allocator> class multiset;
> ^

> In file included from pvec.cpp:21:

> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:44:33: error: no template named 'multiset' in namespace 'std'
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:44:51: error: expected ')'
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:44:27: note: to match this '('
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:51:33: error: reference to 'complex' is ambiguous
> std::size_t hash_value(std::complex<T> const&);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/complex:261:28: note: candidate found by name lookup is
> 'std::__1::complex'
> class _LIBCPP_TEMPLATE_VIS complex
> ^
> ./boost/detail/container_fwd.hpp:69:30: note: candidate found by name lookup is 'std::complex'
> template <class T> class complex;
> ^

> In file included from pvec.cpp:21:

> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:51:33: error: no template named 'complex' in namespace 'std'
> std::size_t hash_value(std::complex<T> const&);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:51:44: error: expected ')'
> std::size_t hash_value(std::complex<T> const&);
> ^
> ./boost/functional/hash/extensions.hpp:51:27: note: to match this '('
> std::size_t hash_value(std::complex<T> const&);
> ^
> ./boost/functional/hash/extensions.hpp:54:33: error: reference to 'pair' is ambiguous
> std::size_t hash_value(std::pair<A, B> const& v)
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/utility:312:29: note: candidate found by name lookup is
> 'std::__1::pair'
> struct _LIBCPP_TEMPLATE_VIS pair
> ^
> ./boost/detail/container_fwd.hpp:90:42: note: candidate found by name lookup is 'std::pair'
> template <class T1, class T2> struct pair;
> ^

> In file included from pvec.cpp:21:

> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:54:33: error: no template named 'pair' in namespace 'std'
> std::size_t hash_value(std::pair<A, B> const& v)
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:54:44: error: expected ')'
> std::size_t hash_value(std::pair<A, B> const& v)
> ^
> ./boost/functional/hash/extensions.hpp:54:27: note: to match this '('
> std::size_t hash_value(std::pair<A, B> const& v)
> ^
> ./boost/functional/hash/extensions.hpp:57:28: error: use of undeclared identifier 'v'
> hash_combine(seed, v.first);
> ^
> fatal error: too many errors emitted, stopping now [-ferror-limit=]
> 20 errors generated.

> In file included from papara2_main.cpp:25:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:34:33: error: reference to 'pair' is ambiguous
> std::size_t hash_value(std::pair<A, B> const&);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/utility:312:29: note: candidate found by name lookup is
> 'std::__1::pair'
> struct _LIBCPP_TEMPLATE_VIS pair
> ^
> ./boost/detail/container_fwd.hpp:90:42: note: candidate found by name lookup is 'std::pair'
> template <class T1, class T2> struct pair;
> ^

> In file included from papara2_main.cpp:25:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:34:33: error: no template named 'pair' in namespace 'std'
> std::size_t hash_value(std::pair<A, B> const&);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:34:44: error: expected ')'
> std::size_t hash_value(std::pair<A, B> const&);
> ^
> ./boost/functional/hash/extensions.hpp:34:27: note: to match this '('
> std::size_t hash_value(std::pair<A, B> const&);
> ^
> ./boost/functional/hash/extensions.hpp:36:33: error: reference to 'vector' is ambiguous
> std::size_t hash_value(std::vector<T, A> const&);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1407:74: note: candidate found by name lookup is
> 'std::__1::vector'
> template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
> ^
> ./boost/detail/container_fwd.hpp:80:47: note: candidate found by name lookup is 'std::vector'
> template <class T, class Allocator> class vector;
> ^

> In file included from papara2_main.cpp:25:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:36:33: error: no template named 'vector' in namespace 'std'
> std::size_t hash_value(std::vector<T, A> const&);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:36:46: error: expected ')'
> std::size_t hash_value(std::vector<T, A> const&);
> ^
> ./boost/functional/hash/extensions.hpp:36:27: note: to match this '('
> std::size_t hash_value(std::vector<T, A> const&);
> ^
> ./boost/functional/hash/extensions.hpp:38:33: error: reference to 'list' is ambiguous
> std::size_t hash_value(std::list<T, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/list:805:28: note: candidate found by name lookup is
> 'std::__1::list'
> class _LIBCPP_TEMPLATE_VIS list
> ^
> ./boost/detail/container_fwd.hpp:79:47: note: candidate found by name lookup is 'std::list'
> template <class T, class Allocator> class list;
> ^

> In file included from papara2_main.cpp:25:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:38:33: error: no template named 'list' in namespace 'std'
> std::size_t hash_value(std::list<T, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:38:44: error: expected ')'
> std::size_t hash_value(std::list<T, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:38:27: note: to match this '('
> std::size_t hash_value(std::list<T, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:40:33: error: reference to 'deque' is ambiguous
> std::size_t hash_value(std::deque<T, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/deque:1187:28: note: candidate found by name lookup is
> 'std::__1::deque'
> class _LIBCPP_TEMPLATE_VIS deque
> ^
> ./boost/detail/container_fwd.hpp:76:47: note: candidate found by name lookup is 'std::deque'
> template <class T, class Allocator> class deque;
> ^

> In file included from papara2_main.cpp:25:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:40:33: error: no template named 'deque' in namespace 'std'
> std::size_t hash_value(std::deque<T, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:40:45: error: expected ')'
> std::size_t hash_value(std::deque<T, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:40:27: note: to match this '('
> std::size_t hash_value(std::deque<T, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:42:33: error: reference to 'set' is ambiguous
> std::size_t hash_value(std::set<K, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/set:400:28: note: candidate found by name lookup is
> 'std::__1::set'
> class _LIBCPP_TEMPLATE_VIS set
> ^
> ./boost/detail/container_fwd.hpp:84:64: note: candidate found by name lookup is 'std::set'
> template <class Key, class Compare, class Allocator> class set;
> ^

> In file included from papara2_main.cpp:25:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:42:33: error: no template named 'set' in namespace 'std'
> std::size_t hash_value(std::set<K, C, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:42:46: error: expected ')'
> std::size_t hash_value(std::set<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:42:27: note: to match this '('
> std::size_t hash_value(std::set<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:44:33: error: reference to 'multiset' is ambiguous
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/set:809:28: note: candidate found by name lookup is
> 'std::__1::multiset'
> class _LIBCPP_TEMPLATE_VIS multiset
> ^
> ./boost/detail/container_fwd.hpp:85:64: note: candidate found by name lookup is 'std::multiset'
> template <class Key, class Compare, class Allocator> class multiset;
> ^

> In file included from papara2_main.cpp:25:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:44:33: error: no template named 'multiset' in namespace 'std'
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:44:51: error: expected ')'
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:44:27: note: to match this '('
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:46:33: error: reference to 'map' is ambiguous
> std::size_t hash_value(std::map<K, T, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__tree:1490:77: note: candidate found by name lookup is
> 'std::__1::map'
> template <class, class, class, class> friend class _LIBCPP_TEMPLATE_VIS map;
> ^
> ./boost/detail/container_fwd.hpp:81:73: note: candidate found by name lookup is 'std::map'
> template <class Key, class T, class Compare, class Allocator> class map;
> ^
> fatal error: too many errors emitted, stopping now [-ferror-limit=]
> 20 errors generated.

> In file included from blast_partassign.cpp:13:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:34:33: error: reference to 'pair' is ambiguous
> std::size_t hash_value(std::pair<A, B> const&);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/utility:312:29: note: candidate found by name lookup is
> 'std::__1::pair'
> struct _LIBCPP_TEMPLATE_VIS pair
> ^
> ./boost/detail/container_fwd.hpp:90:42: note: candidate found by name lookup is 'std::pair'
> template <class T1, class T2> struct pair;
> ^

> In file included from blast_partassign.cpp:13:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:34:33: error: no template named 'pair' in namespace 'std'
> std::size_t hash_value(std::pair<A, B> const&);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:34:44: error: expected ')'
> std::size_t hash_value(std::pair<A, B> const&);
> ^
> ./boost/functional/hash/extensions.hpp:34:27: note: to match this '('
> std::size_t hash_value(std::pair<A, B> const&);
> ^
> ./boost/functional/hash/extensions.hpp:36:33: error: reference to 'vector' is ambiguous
> std::size_t hash_value(std::vector<T, A> const&);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iterator:1407:74: note: candidate found by name lookup is
> 'std::__1::vector'
> template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
> ^
> ./boost/detail/container_fwd.hpp:80:47: note: candidate found by name lookup is 'std::vector'
> template <class T, class Allocator> class vector;
> ^

> In file included from blast_partassign.cpp:13:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:36:33: error: no template named 'vector' in namespace 'std'
> std::size_t hash_value(std::vector<T, A> const&);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:36:46: error: expected ')'
> std::size_t hash_value(std::vector<T, A> const&);
> ^
> ./boost/functional/hash/extensions.hpp:36:27: note: to match this '('
> std::size_t hash_value(std::vector<T, A> const&);
> ^
> ./boost/functional/hash/extensions.hpp:40:33: error: reference to 'deque' is ambiguous
> std::size_t hash_value(std::deque<T, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/deque:1187:28: note: candidate found by name lookup is
> 'std::__1::deque'
> class _LIBCPP_TEMPLATE_VIS deque
> ^
> ./boost/detail/container_fwd.hpp:76:47: note: candidate found by name lookup is 'std::deque'
> template <class T, class Allocator> class deque;
> ^

> In file included from blast_partassign.cpp:13:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:40:33: error: no template named 'deque' in namespace 'std'
> std::size_t hash_value(std::deque<T, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:40:45: error: expected ')'
> std::size_t hash_value(std::deque<T, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:40:27: note: to match this '('
> std::size_t hash_value(std::deque<T, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:42:33: error: reference to 'set' is ambiguous
> std::size_t hash_value(std::set<K, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/set:400:28: note: candidate found by name lookup is
> 'std::__1::set'
> class _LIBCPP_TEMPLATE_VIS set
> ^
> ./boost/detail/container_fwd.hpp:84:64: note: candidate found by name lookup is 'std::set'
> template <class Key, class Compare, class Allocator> class set;
> ^

> In file included from blast_partassign.cpp:13:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:42:33: error: no template named 'set' in namespace 'std'
> std::size_t hash_value(std::set<K, C, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:42:46: error: expected ')'
> std::size_t hash_value(std::set<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:42:27: note: to match this '('
> std::size_t hash_value(std::set<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:44:33: error: reference to 'multiset' is ambiguous
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/set:809:28: note: candidate found by name lookup is
> 'std::__1::multiset'
> class _LIBCPP_TEMPLATE_VIS multiset
> ^
> ./boost/detail/container_fwd.hpp:85:64: note: candidate found by name lookup is 'std::multiset'
> template <class Key, class Compare, class Allocator> class multiset;
> ^

> In file included from blast_partassign.cpp:13:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:44:33: error: no template named 'multiset' in namespace 'std'
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:44:51: error: expected ')'
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:44:27: note: to match this '('
> std::size_t hash_value(std::multiset<K, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:46:33: error: reference to 'map' is ambiguous
> std::size_t hash_value(std::map<K, T, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__tree:1490:77: note: candidate found by name lookup is
> 'std::__1::map'
> template <class, class, class, class> friend class _LIBCPP_TEMPLATE_VIS map;
> ^
> ./boost/detail/container_fwd.hpp:81:73: note: candidate found by name lookup is 'std::map'
> template <class Key, class T, class Compare, class Allocator> class map;
> ^

> In file included from blast_partassign.cpp:13:

> In file included from ./papara.h:47:
> In file included from ./pvec.h:41:
> In file included from ivy_mike/src/ivymike/tree_traversal_utils.h:30:
> In file included from ./boost/tr1/unordered_set.hpp:21:
> In file included from ./boost/unordered_set.hpp:16:
> In file included from ./boost/unordered/unordered_set.hpp:17:
> In file included from ./boost/functional/hash.hpp:6:
> In file included from ./boost/functional/hash/hash.hpp:477:
> ./boost/functional/hash/extensions.hpp:46:33: error: no template named 'map' in namespace 'std'
> std::size_t hash_value(std::map<K, T, C, A> const& v);
> ~~~~~^
> ./boost/functional/hash/extensions.hpp:46:49: error: expected ')'
> std::size_t hash_value(std::map<K, T, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:46:27: note: to match this '('
> std::size_t hash_value(std::map<K, T, C, A> const& v);
> ^
> ./boost/functional/hash/extensions.hpp:48:33: error: reference to 'multimap' is ambiguous
> std::size_t hash_value(std::multimap<K, T, C, A> const& v);
> ~~~~~^
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__tree:1491:77: note: candidate found by name lookup is
> 'std::__1::multimap'
> template <class, class, class, class> friend class _LIBCPP_TEMPLATE_VIS multimap;
> ^
> ./boost/detail/container_fwd.hpp:83:11: note: candidate found by name lookup is 'std::multimap'
> class multimap;
> ^
> fatal error: too many errors emitted, stopping now [-ferror-limit=]
> 20 errors generated.

[cmc...@uw.edu]

After lots and lots of experimentation, I found one approach that worked for me. 

I installed boost version 1.64 with conda, then soft linked the boost includes directory to the papara build directory.

Things that didn't work to allow me to build papapra:

• Building boost 1.68 from source
  
• Building boost 1.41 from source
  
• Building boost 1.64 from source
  
• Installing boost 1.68 with conda
• Installing boost with Mac Ports
• Installing boost with Homebrew
• Linking to the boost include directory using '-I /path/to/boost'

Glad I figured out a workaround, though I'm not sure why this is so difficult. Hope this helps someone in the future. 

best,

Cedar

[Alexandros Stamatakis]

many thanks for sharing this :-)

alexis

On 07.09.2018 00:51, cmc...@uw.edu wrote:
> After lots and lots of experimentation, I found one approach that worked
> for me.
>
> I installed boost version 1.64 with conda, then soft linked the boost
> includes directory to the papara build directory.
>
> Things that didn't work to allow me to build papapra:
>

> * Building boost 1.68 from source
> * Building boost 1.41 from source
> * Building boost 1.64 from source
> * Installing boost 1.68 with conda
> * Installing boost with Mac Ports
> * Installing boost with Homebrew
> * Linking to the boost include directory using '-I /path/to/boost'

>
> Glad I figured out a workaround, though I'm not sure why this is so
> difficult. Hope this helps someone in the future.
>
> best,
> Cedar
>
>

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[Lucas Czech]

Thanks, Cedar, for your effort!

I also remember that it was quite some pain to get this to work! Boost
is a bit tricky sometimes - and PaPaRa also doesn't make it straight
forward... :-(

I guess the soft link solution is the most stable one. Will keep this in
mind, thanks!

Lucas

[cmc...@uw.edu]

Hello Alexis, 

Are there any plans to "freshen up" PaPaRa? Not necessarily updated functionality, but to get it compiling nicely, and the binaries working?

Known issues:

Doesn't compile on latest version of Ubuntu

Difficult to compile on Mac

Mac Binary doesn't work for me

Linux Binary single threaded only

We really like PaPaRa, but it is getting painful to use and recommend on newer operating systems.

Thanks again for all your work.

[Alexandros Stamatakis]

We are currently working on an improved version with a main focus on
improving speed, but will try to have a look at the issue you report
while at it.

Alexis

[cmc...@uw.edu]

Oh, that is good news! Will it continue as a stand-alone product, or be incorporated as a component into another product?

Thanks!

Cedar

[Alexandros Stamatakis]

Dear Cedar,

We don't know yet, the new/improved version is too early in its
development at present.

Alexis