Bio/Entrez/DTDs/modules.ent | 7 0 + 7 - 0 !
1 file changed, 7 deletions(-)

 remove non dfsg free dtd

Tests/Blast/html_msgid_29_blastx_001.html | 5 2 + 3 - 0 !
1 file changed, 2 insertions(+), 3 deletions(-)

 do not use privacy-breach-logo

Doc/cookbook/Restriction/Restriction.html | 3 0 + 3 - 0 !
1 file changed, 3 deletions(-)

 fix privacy breach with html5shiv
 Actually the script called is commented out, except when reading the page with
 Internet Explorer 9.  This patch makes sure the script is not called at all,
 even if it is very unlikely that HTML document installed in Debian will ever
 be read with this browser.

Bio/Blast/Applications.py | 8 8 + 0 - 0 !
1 file changed, 8 insertions(+)

 implement blast database version 4 switch
 This patch adds support for the -blastdb_version switch of the makeblastdb
 wrapper of the library.  This originates from a workaround to fix a build test
 failure on 32 bit architecture, but the option might be interesting upstream
 as well, hence a separation of the implementation and test.

Doc/Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix use of unversioned 'python' interpreter
 The Doc/Makefile uses python to evaluate the current version of the library in
 order to build the documentation, but the unversioned "python" interpreter is
 not available anymore, at least not in the build context.

Tests/test_phyml_tool.py | 2 2 + 0 - 0 !
1 file changed, 2 insertions(+)

 stabilize the test involving phyml
 On multicore systems, the MPI variant is invoked, which for some reason
 attempts to connect to a running X server, which may not be available on build
 environments.  Forcing to use a single threaded variant, by the means of the
 environment variable PHYMLCPUS, allows one to avoid the message "No protocol
 specified" in the error output, which interferes with the version test.

Bio/Cluster/clustermodule.c | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix lintian message spelling-error-in-binary
 As a side note, lintian reports another spelling error "algorith" in another
 binary, but the matching source code does not show any such issue in strings,
 so it might have been a string sliced at a bad place by the compiler.

Doc/Tutorial.tex | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 make the build reproducible
 This patch removes the last update date, which would correspond to the moment
 when the package was build, and wouldn't be too relevant in the document.
 Focusing on the version number would be a better approach here.  This patch is
 not needed upstream, as it would interfere with development releases, marked
 only with the version "dev", so would benefit of the date here.

Bio/PDB/DSSP.py | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 port pdb dssp module to use dssp version 4