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Bug 564749 - FTBFS python-biopython-1.53-1.fc13
Summary: FTBFS python-biopython-1.53-1.fc13
Keywords:
Status: CLOSED NOTABUG
Alias: None
Product: Fedora
Classification: Fedora
Component: python-biopython
Version: rawhide
Hardware: All
OS: Linux
high
high
Target Milestone: ---
Assignee: Alex Lancaster
QA Contact: Fedora Extras Quality Assurance
URL: http://linux.dell.com/files/fedora/Fi...
Whiteboard:
Depends On:
Blocks: F13FTBFS
TreeView+ depends on / blocked
 
Reported: 2010-02-13 16:48 UTC by FTBFS
Modified: 2010-02-21 06:03 UTC (History)
2 users (show)

Fixed In Version:
Doc Type: Bug Fix
Doc Text:
Clone Of:
Environment:
Last Closed: 2010-02-20 08:53:23 UTC
Type: ---
Embargoed:

Attachments (Terms of Use)
root.log (93.50 KB, text/plain)
2010-02-13 16:48 UTC, FTBFS 		no flags Details
build.log (3.68 KB, text/plain)
2010-02-13 16:48 UTC, FTBFS 		no flags Details
mock.log (1.04 KB, text/plain)
2010-02-13 16:48 UTC, FTBFS 		no flags Details
root.log (107.30 KB, text/plain)
2010-02-13 16:48 UTC, FTBFS 		no flags Details
build.log (3.67 KB, text/plain)
2010-02-13 16:48 UTC, FTBFS 		no flags Details
mock.log (992 bytes, text/plain)
2010-02-13 16:48 UTC, FTBFS 		no flags Details
View All

Description FTBFS 2010-02-13 16:48:02 UTC 
python-biopython-1.53-1.fc13.src.rpm Failed To Build From Source against the rawhide tree.  See http://fedoraproject.org/wiki/FTBFS for more information.
If you believe this is actually a bug in another package, do NOT change the component in this bug or close this bug.  Instead, add the appropriate bug number from the other package to the "Depends on" line in this bug.  If the other package does not yet have a bug created that you think matches, please create one.  Doing so helps us properly track bugs and their dependencies, just as we track package dependencies.  (If you close this bug, and the other package is not fixed before the next FTBFS run, a new bug will get created.  Please follow the above advice to avoid such duplication.)
Comment 1 FTBFS 2010-02-13 16:48:05 UTC 
Created attachment 391511 [details]
root.log

root.log for i386
Comment 2 FTBFS 2010-02-13 16:48:06 UTC 
Created attachment 391512 [details]
build.log

build.log for i386
Comment 3 FTBFS 2010-02-13 16:48:07 UTC 
Created attachment 391513 [details]
mock.log

mock.log for i386
Comment 4 FTBFS 2010-02-13 16:48:09 UTC 
Created attachment 391514 [details]
root.log

root.log for x86_64
Comment 5 FTBFS 2010-02-13 16:48:10 UTC 
Created attachment 391515 [details]
build.log

build.log for x86_64
Comment 6 FTBFS 2010-02-13 16:48:11 UTC 
Created attachment 391516 [details]
mock.log

mock.log for x86_64
Comment 7 Alex Lancaster 2010-02-20 08:53:23 UTC 
OK so this seemed to successfully rebuild in devel / rawhide:

http://koji.fedoraproject.org/koji/taskinfo?taskID=2001100

as well as the "branched" rawhide:

http://koji.fedoraproject.org/koji/taskinfo?taskID=2001123

so I'm closing this as NOTABUG as it's a "bogus" false positive for FTBFS.
Comment 8 Matt Domsch 2010-02-21 05:14:11 UTC 
This was the failure:

Numerical Python (NumPy) is not installed.
This package is required for many Biopython features.  Please install
it before you install Biopython. You can install Biopython anyway, but
anything dependent on NumPy will not work. If you do this, and later
install NumPy, you should then re-install Biopython.
You can find NumPy at http://numpy.scipy.org
error: Bad exit status from /var/tmp/rpm-tmp.nYhIuY (%build)
RPM build errors:

Now, it may be that something about NumPy was the actual problem, and that by fixing it, also resolves this bug.  But it failed for me _4 times_, in the same way, so it is not a trivial false positive...
Comment 9 Alex Lancaster 2010-02-21 05:49:43 UTC 
numpy is pulled in by the BuildRequires and the build koji (on rawhide) seemed to find it and use it correctly.  Hence I closed the bug.
Comment 10 Alex Lancaster 2010-02-21 05:59:08 UTC 
In your FTBFS test numpy is also pulled in correctly, from mock.log on x86_64:

DEBUG util.py:256:  
  Installing     : numpy-1.4.0-2.fc13.x86_64                              23/23 


but for some reason the Python couldn't see it in your build.   Odd.  In any case it works on koji.
Comment 11 Alex Lancaster 2010-02-21 06:03:51 UTC 
I guess the version is different in my newer build: numpy-1.4.0-4.fc13.x86_64 vs your 1.4.0-2.fc13 version, so, yes something might have changed, although I'm not sure what would cause it not to be detected by biopython.
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