[Biopython] build problem on Ubuntu

[Alan McKay]

Hi folks,

Ubuntu 13.04 and just did "apt-get -y upgrade"
Python 2.7.4
biopython-1.61

root at ofreezertest:~/ofreeze/biopython-1.61# dpkg --list | grep -i ncbi
ii  libncbi6:amd64                     6.1.20120620-2
 amd64        NCBI libraries for biology applications
ii  libvibrant6a:amd64                 6.1.20120620-2
 amd64        NCBI libraries for graphic biology applications
ii  ncbi-blast+                        2.2.27-3
 amd64        next generation suite of BLAST sequence search tools
ii  ncbi-blast+-legacy                 2.2.27-3
 all          NCBI Blast legacy call script
ii  ncbi-data                          6.1.20120620-2
 all          Platform-independent data for the NCBI toolkit
ii  ncbi-epcr                          2.3.12-1-1
 amd64        Tool to test a DNA sequence for the presence of sequence
tagged sites
ii  ncbi-rrna-data                     6.1.20120620-2
 all          large rRNA BLAST databases distributed with the NCBI
toolkit
ii  ncbi-tools-bin                     6.1.20120620-2
 amd64        NCBI libraries for biology applications (text-based
utilities)
ii  ncbi-tools-x11                     6.1.20120620-2
 amd64        NCBI libraries for biology applications (X-based
utilities)
root at ofreezertest:~/ofreeze/biopython-1.61#


I do the :
python setup.py build

and then the
python setup.py test

It starts going through a bunch of tests - most are ok some are not
but no big deal until a whole bunch of these :

Bio.PDB.Polypeptide docstring test ... ok
Bio.PDB.Selection docstring test ... ok
======================================================================
ERROR: test_write_multiple_from_blastxml
(test_SearchIO_write.BlastXmlWriteCases)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries
(xml_2226_blastp_001.xml)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_SearchIO_write.py", line 55, in test_write_multiple_from_blastxml
    self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
  File "test_SearchIO_write.py", line 27, in parse_write_and_compare
    SearchIO.write(source_qresults, out_file, out_format, **kwargs)
  File "/root/ofreeze/biopython-1.61/build/lib.linux-x86_64-2.7/Bio/SearchIO/__init__.py",
line 610, in write
    writer.write_file(qresults)
  File "/root/ofreeze/biopython-1.61/build/lib.linux-x86_64-2.7/Bio/SearchIO/BlastIO/blast_xml.py",
line 695, in write_file
    xml.startDocument()
  File "/root/ofreeze/biopython-1.61/build/lib.linux-x86_64-2.7/Bio/SearchIO/BlastIO/blast_xml.py",
line 612, in startDocument
    self.write('<?xml version="1.0"?>\n'
  File "/usr/lib/python2.7/xml/sax/saxutils.py", line 103, in write
    super(UnbufferedTextIOWrapper, self).write(s)
TypeError: must be unicode, not str

======================================================================
ERROR: test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query
(xml_2226_blastp_004.xml)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_SearchIO_write.py", line 49, in test_write_single_from_blastxml
    self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
  File "test_SearchIO_write.py", line 27, in parse_write_and_compare
    SearchIO.write(source_qresults, out_file, out_format, **kwargs)
  File "/root/ofreeze/biopython-1.61/build/lib.linux-x86_64-2.7/Bio/SearchIO/__init__.py",
line 610, in write
    writer.write_file(qresults)
  File "/root/ofreeze/biopython-1.61/build/lib.linux-x86_64-2.7/Bio/SearchIO/BlastIO/blast_xml.py",
line 695, in write_file
    xml.startDocument()
  File "/root/ofreeze/biopython-1.61/build/lib.linux-x86_64-2.7/Bio/SearchIO/BlastIO/blast_xml.py",
line 612, in startDocument
    self.write('<?xml version="1.0"?>\n'
  File "/usr/lib/python2.7/xml/sax/saxutils.py", line 103, in write
    super(UnbufferedTextIOWrapper, self).write(s)
TypeError: must be unicode, not str




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