'curl' build on Ubuntu fails with athr_export.h: No such file or directory

[CarlKCarlK]

Greetings, When I try to build via the curl command on Ubuntu (under Windows), I get a messing header message.

(base) carlk@kadie2:/mnt/d/OneDrive/programs/bgen-reader-py2$ curl -fsSL https://git.io/JerYI | GITHUB_USER=limix GITHUB
_PROJECT=bgen bash
[0/7] Library(bgen==3.0.3)
[1/7] Downloading... done.
[2/7] Extracting... done.
[3/7] Configuring... done.
[4/7] Compiling... FAILED.
[_/7] Log output:

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   117  100   117    0     0     20      0  0:00:05  0:00:05 --:--:--    27
100 5398k    0 5398k    0     0   423k      0 --:--:--  0:00:12 --:--:-- 1238k
-------------------------------------------------------------------------------
Hello there. This is the bgen (3.0.3) project. We wish you an easy ride.
If by any chance you find in trouble, please, do not hesitate in contacting
us at <https://github.com/limix/bgen/issues/new>.
-------------------------------------------------------------------------------
-- The C compiler identification is GNU 7.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
-- Found ZSTD: /usr/lib/x86_64-linux-gnu/libzstd.so
-- Found ATHR: /usr/local/lib/libathr.so
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/tmp.19yjgzVBvDbgen/bgen-3.0.3/build
Scanning dependencies of target bgen_static
[  1%] Building C object CMakeFiles/bgen_static.dir/src/depr/buffer.c.o
In file included from /tmp/tmp.19yjgzVBvDbgen/bgen-3.0.3/src/depr/buffer.c:2:0:
/usr/local/include/athr.h:20:10: fatal error: athr_export.h: No such file or directory
 #include "athr_export.h"
          ^~~~~~~~~~~~~~~
compilation terminated.
CMakeFiles/bgen_static.dir/build.make:62: recipe for target 'CMakeFiles/bgen_static.dir/src/depr/buffer.c.o' failed
make[2]: *** [CMakeFiles/bgen_static.dir/src/depr/buffer.c.o] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/bgen_static.dir/all' failed
make[1]: *** [CMakeFiles/bgen_static.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2

Log file path: /tmp/tmp.iB1yutn3MHbgen.log

I then tried building the 'almost there' project first. That project worked, but did not fix the missing header when building bgen.

Thanks, Carl

[CarlKCarlK]

More info:

Summary:

Works on Durbin, but on Ubuntu is installing athr.h, but not athr_export.h

Details:

I was able to get everything working on Durbin under Windows (after installing cmake, zlib, zstd, and athr) I notice that on Durbin the /user/lib/include looks like:

(base) carlk@kadie2:~$ ls /usr/local/include
athr_export.h  athr.h  bgen  bgen.h  zbuff.h  zdict.h  zstd_errors.h  zstd.h

On Ubuntu, I see only athr.h:

(base) carlk@kadie2:~$ ls /usr/local/include
athr.h

When I remove that header file and reinstall athr, I still don't see the expected athr_export.h:

(base) carlk@kadie2:~$ sudo mv /usr/local/include/athr.h ignoreathr.h
(base) carlk@kadie2:~$ curl -fsSL https://git.io/JerYI | GITHUB_USER=horta GITHUB_PROJECT=almosthere DO_CMD=sudo bash
[0/7] Library(almosthere==1.0.15)
[1/7] Downloading... done.
[2/7] Extracting... done.
[3/7] Configuring... done.
[4/7] Compiling... done.
[5/7] Testing... done.
[6/7] Installing...
[ 60%] Built target athr
[ 70%] Built target test_example3
[ 80%] Built target test_example2
[ 90%] Built target test_example4
[100%] Built target test_example1
Install the project...
-- Install configuration: "Release"
-- Installing: /usr/local/lib/libathr.so.1.0.14
-- Up-to-date: /usr/local/lib/libathr.so.1
-- Up-to-date: /usr/local/lib/libathr.so
-- Set runtime path of "/usr/local/lib/libathr.so.1.0.14" to "/usr/local/lib"
-- Installing: /usr/local/include/athr.h
-- Installing: /usr/local/lib/cmake/athr/athr-targets.cmake
-- Installing: /usr/local/lib/cmake/athr/athr-targets-release.cmake
-- Installing: /usr/local/lib/cmake/athr/athr-config.cmake
-- Up-to-date: /usr/local/lib/cmake/athr/librt/FindLibRt.cmake
done.
[7/7] Finalizing... done.
(base) carlk@kadie2:~$ ls /usr/local/include
athr.h

[horta]

Closing as I think we have fixed it.