Hi Afif, On Sun, Dec 06, 2015 at 01:41:43PM -0800, Afif Elghraoui wrote: > > I sent an email around the same time as yours announcing the patch is in > > git. I didn't realize this was the central issue of the bug report. If > > that's the case, I think you should just add the "Closes..." statement > > to the changelog. :) > > > > Yes, this isn't the central issue of the bug report, but we are now back > to the original status, but there are at least no additional test > failures on i386 than what was originally reported.
Hmmm, I have seen commit 7c93b9c0d42c415ef3296e6ee4a7d61b6fc34cb8 but I remain with failures even on amd64. :-( ... I: VER=0.6.1p1 python2.7 test/test.py Doctest of tss.rst: ********************************************************************** File "../doc/tss.rst", line 41, in tss.rst Failed example: for almnt in bamfile: if almnt.aligned: coverage[ almnt.iv ] += 1 Exception raised: Traceback (most recent call last): File "/usr/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest tss.rst[4]>", line 1, in <module> for almnt in bamfile: File "/build/htseq-0.6.1p1/build/lib.linux-x86_64-2.7/HTSeq/__init__.py", line 943, in __iter__ sf = pysam.AlignmentFile(self.filename, "rb") AttributeError: 'module' object has no attribute 'AlignmentFile' ********************************************************************** File "../doc/tss.rst", line 211, in tss.rst Failed example: for almnt in sortedbamfile[ window ]: print almnt #doctest:+ELLIPSIS +NORMALIZE_WHITESPACE Exception raised: Traceback (most recent call last): File "/usr/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest tss.rst[27]>", line 1, in <module> for almnt in sortedbamfile[ window ]: File "/build/htseq-0.6.1p1/build/lib.linux-x86_64-2.7/HTSeq/__init__.py", line 975, in __getitem__ self.sf = pysam.AlignmentFile( self.filename, "rb" ) AttributeError: 'module' object has no attribute 'AlignmentFile' ********************************************************************** File "../doc/tss.rst", line 220, in tss.rst Failed example: almnt.iv.length = fragmentsize Exception raised: Traceback (most recent call last): File "/usr/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest tss.rst[29]>", line 1, in <module> almnt.iv.length = fragmentsize NameError: name 'almnt' is not defined ... ********************************************************************** File "../doc/tss.rst", line 331, in tss.rst Failed example: almnt.iv.length = fragmentsize Exception raised: Traceback (most recent call last): File "/usr/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest tss.rst[42]>", line 1, in <module> almnt.iv.length = fragmentsize NameError: name 'almnt' is not defined ********************************************************************** File "../doc/tss.rst", line 332, in tss.rst Failed example: almnt Exception raised: Traceback (most recent call last): File "/usr/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest tss.rst[43]>", line 1, in <module> almnt NameError: name 'almnt' is not defined ********************************************************************** 1 items had failures: 11 of 37 in tss.rst ***Test Failed*** 11 failures. 11 of 37 tests failed. Doctest of overview.rst: All 0 tests passed. Doctest of tour.rst: ********************************************************************** File "../doc/tour.rst", line 189, in tour.rst Failed example: for a in itertools.islice( bam_reader, 5 ): # printing first 5 reads print a Exception raised: Traceback (most recent call last): File "/usr/lib/python2.7/doctest.py", line 1315, in __run compileflags, 1) in test.globs File "<doctest tour.rst[22]>", line 1, in <module> for a in itertools.islice( bam_reader, 5 ): # printing first 5 reads File "/build/htseq-0.6.1p1/build/lib.linux-x86_64-2.7/HTSeq/__init__.py", line 943, in __iter__ sf = pysam.AlignmentFile(self.filename, "rb") AttributeError: 'module' object has no attribute 'AlignmentFile' ********************************************************************** 1 items had failures: 1 of 80 in tour.rst ***Test Failed*** 1 failures. 1 of 80 tests failed. Strange that you can not reproduce this. Kind regards Andreas. -- http://fam-tille.de