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Re: CMake help: pthread linking issue

Hi Sascha,

thanks a lot for working on this.  That's really appreciated since salmon
upgrades always turn out to be a bit rough compared to other packages.

On Wed, May 09, 2018 at 11:41:11AM +0200, Sascha Steinbiss wrote:
> Someone showed me how I waved my hand in the wrong direction while
> spellcasting ;) So I managed to get around that particular issue now and
> also updated the embedded copy of RapMap that is sadly still required to
> build to the same version currently in unstable.
> Unfortunately I am now stuck with another fairly cryptic (to me) build
> failure regarding spdlog:

There is another one before this:

/build/salmon-0.8.0+ds1/src/SalmonQuantifyAlignments.cpp: In function 'int salmonAlignmentQuantify(int, char**)':
/build/salmon-0.8.0+ds1/src/SalmonQuantifyAlignments.cpp:1574:73: error: no matching function for call to 'make_shared<template<class Mutex> class spdlog::sinks::ansicolor_sink>(std::shared_ptr<spdlog::sinks::st
derr_sink<std::mutex> >&)'
In file included from /usr/include/c++/7/memory:81:0,

> /usr/include/c++/7/bits/shared_ptr.h:703:5: note:   template argument
> deduction/substitution failed:
> /build/salmon-0.8.0+ds1/src/SalmonQuantifyAlignments.cpp:1575:69: error:

Since I see 0.8.0 in the version string:  The latest version is 0.9.1.
To save some time it might be sensible to spent it on the latest version
and not on some intermediate version that by chance was the last one
somebody was fighting with and thus is residing in Git.

> no matching function for call to 'create(const char [11],
> <brace-enclosed initializer list>)'
>          auto consoleLog = spdlog::create("consoleLog", {consoleSink});
>                                                                      ^
> In file included from /usr/include/spdlog/spdlog.h:192:0,
>                  from /build/salmon-0.8.0+ds1/include/SalmonOpts.hpp:7,
>                  from /build/salmon-0.8.0+ds1/include/SalmonUtils.hpp:25,
>                  from /build/salmon-0.8.0+ds1/include/Transcript.hpp:10,
>                  from /build/salmon-0.8.0+ds1/include/ClusterForest.hpp:7,
>                  from

> Full build log attached.

I've read it - but that C++ stuff is what I usually bounce to
debian-mentors (and if I'm really happy some from Debian Med answers,
quite frequently Gert Wollny).

> I have also pushed the modified WIP code to
> Salsa's salmon master.
> Also, to get his far I had to disable building the unit tests as
> apparently the rest of the Salmon code wasn't linked against the test
> code at build time. Maybe someone could take another look?
> I am afraid that my current lack of time for diving into CMake/C++
> specific stuff and the fact that I do not use Salmon at all myself are
> not the best foundations for doing this package correctly and at a high
> standard. Does anyone care a bit more about Salmon and might want to
> step in? (probably Kevin or Michael? ;))

Thanks again Sascha.  It would be really great if someone would catch
up - most preferably with the latest upstream version.

Kind regards



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