Ticket #3060 (closed enhancement: fixed)
[with package, positive review] biopython optional package update (to 1.45)
| Reported by: | mhampton | Owned by: | somebody |
|---|---|---|---|
| Priority: | minor | Milestone: | sage-3.0.1 |
| Component: | packages: optional | Keywords: | biopython, biology, packages |
| Cc: | Work issues: | ||
| Report Upstream: | Reviewers: | ||
| Authors: | Merged in: | ||
| Dependencies: | Stopgaps: |
Description
On March 22, 2008, the biopython devs released version 1.45. I have put an updated sage package at: http://www.d.umn.edu/~mhampton/biopython-1.45.spkg
Change History
comment:1 Changed 5 years ago by mhampton
- Summary changed from biopython optional package update (to 1.45) to [with package, needs review - ?] biopython optional package update (to 1.45)
comment:2 Changed 5 years ago by mabshoff
- Summary changed from [with package, needs review - ?] biopython optional package update (to 1.45) to [with package, negative review] biopython optional package update (to 1.45)
Ok, there are a couple issues. For one:
running install_data
running install_egg_info
Removing /scratch/mabshoff/release-cycle/sage-3.0.1.alpha1/local/lib/python2.5/site-packages/egenix_mx_base-2.0.6-py2.5.egg-info
Writing /scratch/mabshoff/release-cycle/sage-3.0.1.alpha1/local/lib/python2.5/site-packages/egenix_mx_base-2.0.6-py2.5.egg-info
running install
Traceback (most recent call last):
File "setup.py", line 545, in <module>
data_files=DATA_FILES,
File "/scratch/mabshoff/release-cycle/sage-3.0.1.alpha1/local/lib/python2.5/distutils/core.py", line 151, in setup
dist.run_commands()
File "/scratch/mabshoff/release-cycle/sage-3.0.1.alpha1/local/lib/python2.5/distutils/dist.py", line 974, in run_commands
self.run_command(cmd)
File "/scratch/mabshoff/release-cycle/sage-3.0.1.alpha1/local/lib/python2.5/distutils/dist.py", line 994, in run_command
cmd_obj.run()
File "setup.py", line 147, in run
if check_dependencies_once():
File "setup.py", line 65, in check_dependencies_once
_CHECKED = check_dependencies()
File "setup.py", line 89, in check_dependencies
if is_installed_fn():
File "setup.py", line 320, in is_mxTextTools_installed
return can_import("mx.TextTools")
File "setup.py", line 275, in can_import
return __import__(module_name)
File "/scratch/mabshoff/release-cycle/sage-3.0.1.alpha1/local/lib/python2.5/site-packages/mx/TextTools/__init__.py", line 8, in <module>
from TextTools import *
File "/scratch/mabshoff/release-cycle/sage-3.0.1.alpha1/local/lib/python2.5/site-packages/mx/TextTools/TextTools.py", line 13, in <module>
from mxTextTools import *
File "/scratch/mabshoff/release-cycle/sage-3.0.1.alpha1/local/lib/python2.5/site-packages/mx/TextTools/mxTextTools/__init__.py", line 12, in <module>
BMS = TextSearch
NameError: name 'TextSearch' is not defined
Error install biopython
real 0m10.058s
user 0m8.569s
sys 0m1.252s
There is also a bunch of OSX indexing crap in the spkg. I fixed those, added an hg repo, checked in everything, added proper "exit 1" in two places in case the install failed. What seems to cause the above failure in an installed biopython-1.44. Fixing this requires nuking
rm -rf mx/ Bio Martel/ BioSQL/ biopython-1.44-py2.5.egg-info egenix_mx_base-*
in $SAGE_LOCAL/lib/python2.5/site-packages/ - I am fixing this in the spkg-install and will take half the credit for this spkg since I am a mean, mean guy ;)
Cheers,
Michael
comment:3 Changed 5 years ago by mabshoff
- Summary changed from [with package, negative review] biopython optional package update (to 1.45) to [with package, positive review] biopython optional package update (to 1.45)
Ok, all is fixed in
http://sage.math.washington.edu/home/mabshoff/release-cycles-3.0.1/rc0/biopython-1.45.spkg
Positive review and uploading it to the official repo.
Cheers,
Michael
