#184 Bad Proteowizard dependency

[Stephen C]

Hi,
When trying to compile v2.0 or the development version, I'm hitting a wall with the ProteoWizard BOOST dependency. ProteoWizard crashes with

error: ‘uintptr_t’ was not declared in this scope
typedef atomic<uintptr_t> atomic_uintptr_t;</uintptr_t>

which is an issue with BOOST v1.54, and the ProteoWizard folks claimed that they had additional issues with v1.55, so they would wait until v1.56 came out before fixing this. BOOST updated very recently, so is a request to keep an eye out for some ProteoWizard update and consider including it.

[William S Noble]

We think that this problem is compiler specific. If possible, try using gcc4.7 instead of gcc4.8.

The Proteowizard folks tell us that they will be updating to Boost v1.56, which came out earlier this month. When that happens, this problem should also be solved for Crux.

[William S Noble]

In principle, this problem should fix itself once ProteoWizard gets updated. We have pinged them about this several months ago and are just awaiting the update.

[Kaipo]

It looks like ProteoWizard updated to Boost 1.56.0 yesterday:

r6979 | chambm | 2014-12-09 08:15:35 -0800 (Tue, 09 Dec 2014) | 10 lines

- merged changes from VS 2013 branch (through r6948)
- updated pwiz to VS 2013
- updated .NET projects to use 4.5.1 framework
- updated Boost to 1.56.0
- updated Boost.Build to support VC12
- fixed quickbuild.bat to always build to bin.nt whether bjam is built as 32 or 64-bit
- updated WiX installer script and removed installer support for older MSVC versions
- updated ABI, Agilent, and Waters DLLs
- added Baf2Sql for Bruker, which improves performance of reading BAF files (especially after the first time it's accessed); requires VC11 (VS 2012) runtime
- added get<optional<T>> overloads for sqlite3pp

This change seems to cause our build to fail..

[Kaipo]

The build now works with ProteoWizard using Boost 1.56.

[Charles E. Grant]

Unfortunately the Windows build still doesn't work.
The first error was that the library MassLynxRaw.lib couldn't be found.
I removed the instructions to link to that library from src/c/CMakeLists.txt.
That removed one error, but then we got several errors about missing symbols related to SQLite. I added instructions to link to the SQLite libraries, and those errors went away, but we're left error messages about missing symbols from baf2sql. PWiz does build baf2sql, but only as a DLL. I'll have to figure the CMake commands to link to a DLL.