[pygr-notify] Issue 137 in pygr: building the docs fails with missing modules (seqfmt, cnestedlist, MySQLdb)

[pygr at googlecode.com]

Status: New
Owner: pygr-bug... at googlegroups.com
Labels: Type-Defect Priority-Medium

New issue 137 by niederst... at gmail.com: building the docs fails with  
missing modules (seqfmt, cnestedlist, MySQLdb)
http://code.google.com/p/pygr/issues/detail?id=137

What steps will reproduce the problem?
1. Build pygr-doc using Fink .info file
2. See error output

What is the expected output? What do you see instead?

This is the error output:

mkdir -p html_new/epydoc
epydoc --docformat restructuredtext ../pygr -o html_new/epydoc
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| In /sw32/build.build/pygr-doc-0.8.1-1/pygr-0.8.1/pygr/translationDB.py:
| Import failed (but source code parsing was successful).
|     Error: ImportError: No module named seqfmt (line 1)
|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| In /sw32/build.build/pygr-doc-0.8.1-1/pygr-0.8.1/pygr/seqdb.py:
| Import failed (but source code parsing was successful).
|     Error: ImportError: No module named seqfmt (line 154)
|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| In /sw32/build.build/pygr-doc-0.8.1-1/pygr-0.8.1/pygr/xnestedlist.py:
| Import failed (but source code parsing was successful).
|     Error: ImportError: No module named cnestedlist (line 1)
|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| In /sw32/build.build/pygr-doc-0.8.1-1/pygr-0.8.1/pygr/blast.py:
| Import failed (but source code parsing was successful).
|     Error: ImportError: No module named seqfmt (line 8)
|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| In /sw32/build.build/pygr-doc-0.8.1-1/pygr-0.8.1/pygr/apps/__init__.py:
| Import failed (but source code parsing was successful).
|     Error: ImportError: No module named MySQLdb (line 1)
|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| In /sw32/build.build/pygr-doc-0.8.1-1/pygr-0.8.1/pygr/apps/leelabdb.py:
| Import failed (but source code parsing was successful).
|     Error: ImportError: No module named MySQLdb (line 1)
|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| In /sw32/build.build/pygr-doc-0.8.1-1/pygr-0.8.1/pygr/apps/maf2nclist.py:
| Import failed (but source code parsing was successful).
|     Error: ImportError: No module named MySQLdb (line 1)
|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| In /sw32/build.build/pygr-doc-0.8.1-1/pygr-0.8.1/pygr/apps/seqref.py:
| Import failed (but source code parsing was successful).
|     Error: ImportError: No module named MySQLdb (line 1)
|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| In /sw32/build.build/pygr-doc-0.8.1-1/pygr-0.8.1/pygr/apps/splicegraph.py:
| Import failed (but source code parsing was successful).
|     Error: ImportError: No module named MySQLdb (line 1)
|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| In  
/sw32/build.build/pygr-doc-0.8.1-1/pygr-0.8.1/pygr/apps/catalog_downloads.py:
| Import failed (but source code parsing was successful).
|     Error: ImportError: No module named MySQLdb (line 1)
|
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| In /sw32/build.build/pygr-doc-0.8.1-1/pygr-0.8.1/pygr/apps/maf2VSgraph.py:
| Import failed (but source code parsing was successful).
|     Error: ImportError: No module named MySQLdb (line 1)
|
Warning: No information available for pygr.xnestedlist.NLMSAClient's base  
cnestedlist.NLMSA
Warning: No information available for pygr.xnestedlist.NLMSAServer's base  
cnestedlist.NLMSA
        
00:04                                                                                 
Progress:                                                                                 
00:10
  28%  
[===================================================--------------------------------------------------------------------------------------------------------------------------------]
                                                                                   
Parsing  
docstrings: basestring

UNEXPECTED ERROR:
'Text' object has no attribute 'data'

Use --debug to see trace information.
make: *** [epydocs] Error 3


What version of the product are you using? On what operating system?
0.8.2, but also happens on 0.8.1.  Tested on OS X 10.6 under both 32 and  
64bit installs.

Please provide any additional information below.

See  
<http://sourceforge.net/tracker/?func=detail&atid=414256&aid=3139092&group_id=17203>  
for the Fink tracker entry for this.