[Debian-med-packaging] Bug#833288: would FTBFS now with cython 0.24.1 MACS2/IO/PeakIO.pyx:632:49: Cannot assign type 'float' to 'int'

[Andreas Tille]

Hi,

I can confirm this bug.

I've checked MACS2/IO/PeakIO.pyx and I think the typing of the function
call should be fine - so probably the problem is somewhere else - but
where?

Any help would be welcome

      Andreas.

On Tue, Aug 02, 2016 at 10:37:50AM -0400, Yaroslav Halchenko wrote:
> Package: macs
> Version: 2.1.1.20160309-1
> Severity: serious
> Tags: upstream
> Justification: fails to build from source (but built successfully in the past)
> 
> I have just uploaded cython 0.24.1 into sid and while testing reverse build
> depends found that macs fails to build.  Here is the log extract:
> 
> building 'MACS2.Signal' extension
> x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c MACS2/Signal.c -o build/temp.linux-x86_64-2.7/MACS2/Signal.o -w -O3 -ffast-math
> x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-2.7/MACS2/Signal.o -o /build/macs-2.1.1.20160309/.pybuild/pythonX.Y_2.7/build/MACS2/Signal.so
> cythoning MACS2/IO/PeakIO.pyx to MACS2/IO/PeakIO.c
> 
> Error compiling Cython file:
> ------------------------------------------------------------
> ...
>             pileup = float(fields[5])
>             pscore = float(fields[6])
>             fc = float(fields[7])
>             qscore = float(fields[8])
>             peakname = rstrip(fields[9])
>             add(chrom, start, end, summit, qscore, pileup, pscore, fc, qscore,
>                                                 ^
> ------------------------------------------------------------
> 
> MACS2/IO/PeakIO.pyx:632:49: Cannot assign type 'float' to 'int'
> building 'MACS2.IO.PeakIO' extension
> x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c MACS2/IO/PeakIO.c -o build/temp.linux-x86_64-2.7/MACS2/IO/PeakIO.o -w -O3 -ffast-math
> MACS2/IO/PeakIO.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
>  #error Do not use this file, it is the result of a failed Cython compilation.
>   ^
> error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
> E: pybuild pybuild:274: build: plugin distutils failed with: exit code=1: /usr/bin/python setup.py build 
> dh_auto_build: pybuild --build -i python{version} -p 2.7 returned exit code 13
> debian/rules:16: recipe for target 'override_dh_auto_build' failed
> make[1]: *** [override_dh_auto_build] Error 25
> make[1]: Leaving directory '/build/macs-2.1.1.20160309'
> debian/rules:13: recipe for target 'build' failed
> make: *** [build] Error 2
> 
> 
> cheers!
> 
> -- System Information:
> Debian Release: stretch/sid
>   APT prefers testing
>   APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental'), (100, 'unstable-debug')
> Architecture: amd64 (x86_64)
> Foreign Architectures: i386
> 
> Kernel: Linux 4.5.0-1-amd64 (SMP w/4 CPU cores)
> Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
> 
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> 

-- 
http://fam-tille.de