Your message dated Mon, 21 Nov 2016 00:31:39 -0500 with message-id <20161121053139.yuaj7jowd5ov4...@hopa.kiewit.dartmouth.edu> and subject line Re: [Python-apps-team] Bug#833288: would FTBFS now with cython 0.24.1 MACS2/IO/PeakIO.pyx:632:49: Cannot assign type 'float' to 'int' has caused the Debian Bug report #833288, regarding would FTBFS now with cython 0.24.1 MACS2/IO/PeakIO.pyx:632:49: Cannot assign type 'float' to 'int' to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 833288: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=833288 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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)
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--- Begin Message ---Version: 0.25.2~b0-1 fresh cython was uploaded and I am reconfirming that it fixed this FTBFS: macs_2.1.1.20160309-1.dsc FAILED ok so FAILED before and builds now.... so closing this one On Wed, 16 Nov 2016, Gianfranco Costamagna wrote: > Hi, > > I'm currently going to test a build for the attached patch, will upload in > > deferred/5 in case everything is good. > confirmed a successful build with the package on [1]. > dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is > not NFS-safe > dpkg-gencontrol: warning: package macs: unused substitution variable > ${python:Versions} > dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is > not NFS-safe > dpkg-gencontrol: warning: package macs: unused substitution variable > ${python:Versions} > dh_md5sums -O--buildsystem=pybuild > dh_builddeb -O--buildsystem=pybuild > dpkg-deb: building package 'macs-dbgsym' in > '../macs-dbgsym_2.1.1.20160309-1_amd64.deb'. > dpkg-deb: building package 'macs' in '../macs_2.1.1.20160309-1_amd64.deb'. > dpkg-genbuildinfo > dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which > is not NFS-safe > dpkg-genchanges >../macs_2.1.1.20160309-1_amd64.changes > dpkg-genchanges: info: including full source code in upload > dpkg-source --after-build macs-2.1.1.20160309 > [1] > http://debomatic-amd64.debian.net/distribution#unstable/cython/0.24.1-2.1/buildlog > in deferred/5 -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
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