fails to compile with boost 1.56+

[wookietreiber]

I am on an up to date Arch Linux with boost 1.57.0. cufflinks compilation fails at target abundances.o with the following errors (this is the output of clang++ which I find nicer visually better than g++):

In file included from abundances.cpp:16:
In file included from ./abundances.h:17:
In file included from /usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/vector:60:
In file included from /usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/bits/stl_algobase.h:64:
/usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/bits/stl_pair.h:119:22: error: no matching constructor for initialization of 'boost::shared_ptr<void>'
        : first(__p.first), second(__p.second) { }
                            ^      ~~~~~~~~~~

In file included from abundances.cpp:16:
In file included from ./abundances.h:17:
In file included from /usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/vector:60:
In file included from /usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/bits/stl_algobase.h:64:
/usr/bin/../lib64/gcc/x86_64-unknown-linux-gnu/4.9.2/../../../../include/c++/4.9.2/bits/stl_pair.h:119:22: error: no matching constructor for initialization of 'boost::shared_ptr<void>'
        : first(__p.first), second(__p.second) { }
                            ^      ~~~~~~~~~~

I presume errors like these may occur in other places as well.

[wookietreiber]

I also downgraded boost to 1.56.0 which didn't work either.

[wookietreiber]

On another server I still have a compiled and working cufflinks installation with boost 1.55. This leads me to suspect that the relevant change had been between boost 1.55 and 1.56.

BTW everything has been tried with cufflinks 2.2.1.

[ctrapnell]

Do you still get this error with the HEAD of the develop branch? We've had some issues with Clang and 1.56+, as have a number of other projects. I probably won't get to this until Macports releases their 1.57 portfile, as it seemed like there were a bunch of problems in 1.56, some of which are worked out in 1.57.

[wookietreiber]

Still the same errors with both gcc and clang for HEAD of develop branch.

[apeltzer]

I can confirm this issue, same here.

[sjackman]

I see this issue with boost 1.57 installed on Mac using Homebrew.

[ctrapnell]

This compilation failure results from a bug in Boost serialization in 1.56+ (https://svn.boost.org/trac/boost/ticket/10488). Although there appears to be some disagreement about whether this truly is considered a bug, Cufflinks appears to be one of many programs affected by the shared_ptr serialization policy change. Working around this in Cufflinks looks like it requires that I remove const qualifiers on numerous shared_ptrs, which I'm not willing to do. This will remain open for the time being. Users should stick to Boost 1.55 and lower.

[robertramey]

note this is corrected in the boost master branch and will appear in the next boost release

[smowton]

:D Thanks @robertramey

[ryandesign]

I tested with boost 1.58.0 beta 1, released March 16, 2015, and the problem remains.

[nsoranzo]

Can this be mentioned in http://cole-trapnell-lab.github.io/cufflinks/getting_started/ ? It would save people some time!

And also that samtools needs to be <= 0.1.19 .

[ryandesign]

I tested with boost 1.58.0, released April 17, 2015, and the problem remains.

[ctrapnell]

Apparently the fix didn't take the first time around. Looks like we'll have to wait for 1.59 for the official fix in Boost::Serialization. I will update the getting started page for those who want to build from source.

[mschubert]

1.59 is in beta, did anyone try this already?

[xnox]

https://github.com/boostorg/serialization/commit/010055816681a003a8090d105ea5ab385bb87bf8.patch is the fix, no?

[mschubert]

Just tested on gentoo_prefix with boost=1.59, and it works.

[ctrapnell]

Confirmed - I can also build on OS X via macports' boost 1.59.