libcifpp compilation failed

[rsanchezgarc]

Hi,

I am trying to install xmipp in a new machine and I am getting the following error. I assume is a version issue. Any help here?
My compiler is gcc/++ 11.2

Compiling libcifpp--------
Not trying to recreate symop_table_data.hpp since CCP4 is not defined
-- Testing for known regex bug, since you're using GNU libstdc++
-- You are probably trying to compile using the g++ standard library which contains a crashing std::regex implementation. Will use boost::regex instead
-- Found the following ICU libraries:
-- data (required): /usr/lib64/libicudata.so
-- i18n (required): /usr/lib64/libicui18n.so
-- uc (required): /usr/lib64/libicuuc.so
-- Configuring done (0.3s)

-- Generating done (0.0s)
-- Build files have been written to: /data/nagagpu05/not-backed-up/special-project/app/scipion3/software/em/xmipp/src/libcifpp/build
[ 4%] Building CXX object CMakeFiles/cifpp.dir/src/utilities.cpp.o
[ 9%] Building CXX object CMakeFiles/cifpp.dir/src/point.cpp.o
In file included from /data/nagagpu05/not-backed-up/special-project/app/scipion3/software/em/xmipp/src/libcifpp/src/point.cpp:27:
/data/nagagpu05/not-backed-up/special-project/app/scipion3/software/em/xmipp/src/libcifpp/include/cif++/point.hpp:734:32: error: ‘uint32_t’ has not been declared
734 | const point operator[](uint32_t inIx) const { return m_points[inIx]; }
| ^~~~~~~~
gmake[2]: *** [CMakeFiles/cifpp.dir/build.make:258: CMakeFiles/cifpp.dir/src/point.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:101: CMakeFiles/cifpp.dir/all] Error 2

[MartinSalinas98]

Hey @rsanchezgarc , it might be a std library issue. For me, when I open file xmipp/src/libcifpp/include/cif++/point.hpp in a text editor like VSCode and Ctrl+click on uint32_t in line 734, it takes me to the declaration inside the std library of c++. You might have an older version of that library since your compiler says that there is no declaration of that data type.

If you are on a Debian based distro (like Ubuntu), maybe doing sudo apt install libstdc++-11 could fix your issue.

[oxforddwm]

This appears to be caused by point.hpp and its include set not including the directive:

#include <cstdint>

I found that adding this file to the other includes in point.hpp resolved this problem. This may not be the ideal fix, but works for me.

[MartinSalinas98]

@oxforddwm you are probably right. That seems to be a fix for it, since the original developer of the library causing this issue, libcifpp, already implemented this fix in his repo. I'm going to (very carefully) update the fork xmipp uses with the latest changes to make sure they don't break any other thing (like gcc 8 and 9 version compatibility, because the original repo uses very new c++ features that only worked with gcc/g++ in version 10+). As soon as that is done, you can try to reinstall xmipp running:

scipion3 run ./xmipp cleanAll
(type "YeS" when prompted)
scipion3 run ./xmipp

[MartinSalinas98]

It looks like it also adds new dependencies, which is pretty difficult to justify for xmipp, since we try to avoid new depencies if at all costs. So, I'll just copy that change for now.

@rsanchezgarc Try again with the commands I provided in the previous message, it should work now (hopefully).

[rsanchezgarc]

Hi Martin,

Changing the header file was enough to compile it. Though I was not able to cully compile xmipp, but I will open another issue.

[MartinSalinas98]

Okay, so I'm closing this one now