Author: tille Date: 2015-05-12 09:30:16 +0000 (Tue, 12 May 2015) New Revision: 19217
Added: trunk/packages/python-biopython/trunk/debian/patches/privacy_breach.patch Modified: trunk/packages/python-biopython/trunk/debian/README.source trunk/packages/python-biopython/trunk/debian/changelog trunk/packages/python-biopython/trunk/debian/control trunk/packages/python-biopython/trunk/debian/patches/series trunk/packages/python-biopython/trunk/debian/rules Log: Versioned (Build-)Depends: python-rdflib (>= 4), Prevent privacy-breach-logo, Upload to unstable Modified: trunk/packages/python-biopython/trunk/debian/README.source =================================================================== --- trunk/packages/python-biopython/trunk/debian/README.source 2015-05-12 08:22:42 UTC (rev 19216) +++ trunk/packages/python-biopython/trunk/debian/README.source 2015-05-12 09:30:16 UTC (rev 19217) @@ -69,9 +69,4 @@ So the Build-Depends from bwa is only on these architectures and the test is consequently only run there. - -The test test_Phylo_CDAO for Python3 also needs python3-rdflib, but this is -currently only avialable in experimental, so this will be ignored for the -moment. - -- Andreas Tille <[email protected]> Tue, 04 Mar 2014 11:16:02 +0100 Modified: trunk/packages/python-biopython/trunk/debian/changelog =================================================================== --- trunk/packages/python-biopython/trunk/debian/changelog 2015-05-12 08:22:42 UTC (rev 19216) +++ trunk/packages/python-biopython/trunk/debian/changelog 2015-05-12 09:30:16 UTC (rev 19217) @@ -1,9 +1,11 @@ -python-biopython (1.65+dfsg-1) UNRELEASED; urgency=medium +python-biopython (1.65+dfsg-1) unstable; urgency=medium * New upstream version * Apply fix for broken test from Upstream Git + * Versioned (Build-)Depends: python-rdflib (>= 4) + * Prevent privacy-breach-logo - -- Andreas Tille <[email protected]> Sat, 09 May 2015 07:13:03 +0200 + -- Andreas Tille <[email protected]> Tue, 12 May 2015 11:08:43 +0200 python-biopython (1.64+dfsg-5) unstable; urgency=medium Modified: trunk/packages/python-biopython/trunk/debian/control =================================================================== --- trunk/packages/python-biopython/trunk/debian/control 2015-05-12 08:22:42 UTC (rev 19216) +++ trunk/packages/python-biopython/trunk/debian/control 2015-05-12 09:30:16 UTC (rev 19217) @@ -3,7 +3,6 @@ Uploaders: Charles Plessy <[email protected]>, Andreas Tille <[email protected]> Section: python -Testsuite: autopkgtest Priority: optional Build-Depends: debhelper (>= 9), dpkg-dev (>= 1.16.1~), @@ -32,8 +31,8 @@ python3-matplotlib, python-pil, python3-pil, - python-rdflib, - python3-rdflib, + python-rdflib (>= 4), + python3-rdflib (>= 4), python-renderpm, python3-renderpm, python-psycopg2, @@ -73,7 +72,7 @@ python-matplotlib, python-numpy, python-pil, - python-rdflib, + python-rdflib (>= 4), python-renderpm, python-psycopg2, raxml, @@ -122,7 +121,7 @@ python3-matplotlib, python3-numpy, python3-pil, - python3-rdflib, + python3-rdflib (>= 4), python3-renderpm, python3-psycopg2, raxml, Added: trunk/packages/python-biopython/trunk/debian/patches/privacy_breach.patch =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/privacy_breach.patch (rev 0) +++ trunk/packages/python-biopython/trunk/debian/patches/privacy_breach.patch 2015-05-12 09:30:16 UTC (rev 19217) @@ -0,0 +1,23 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Tue, 12 May 2015 11:08:43 +0200 +Description: Do not use privacy-breach-logo + +--- a/Tests/Blast/html_msgid_29_blastx_001.html ++++ b/Tests/Blast/html_msgid_29_blastx_001.html +@@ -42,8 +42,7 @@ + <script language="JavaScript" type="text/javascript"><!-- + // --></script><table class="medium1" style="border:2px solid #336699;" cellpadding="2" cellspacing="0" id="myncbi_off"><tr><td + bgcolor="#336699" align="left"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?";><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td +-bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/"; title="My NCBI help"><img border="0" +-src="http://www.ncbi.nlm.nih.gov/corehtml/query/MyNCBI/myncbihelpicon.gif"; alt="My NCBI help" /></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a ++bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/"; title="My NCBI help">My NCBI help</a></td></tr><tr><td colspan="2" nowrap="nowrap"><a + href="http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FCMD%3DPut%26DATABASE%3Dnr%26ERROR%3DMessage%2BID%252329%2BError%253A%2BQuery%2Bstring%2Bnot%2Bfound%2Bin%2Bthe%2BCGI%2Bcontext%26EXPECT%3D1e%2D07%26HITLIST%5FSIZE%3D10%26MYNCBI%5FUSER%3D%2D1%26MYNCBI%5FUSER%3D%2D1%26PROGRAM%3Dblastx%26QUERY%3D%26USER%5FTYPE%3D0%26USER%5FTYPE%3D0"; title="Click to sign in" + onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FCMD%3DPut%26DATABASE%3Dnr%26ERROR%3DMessage%2BID%252329%2BError%253A%2BQuery%2Bstring%2Bnot%2Bfound%2Bin%2Bthe%2BCGI%2Bcontext%26EXPECT%3D1e%2D07%26HITLIST%5FSIZE%3D10%26MYNCBI%5FUSER%3D%2D1%26MYNCBI%5FUSER%3D%2D1%26PROGRAM%3Dblastx%26QUERY%3D%26USER%5FTYPE%3D0%26USER%5FTYPE%3D0');return false;">[Sign In]</a> <a + href="http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fblast%2Encbi%2Enlm%2Enih%2Egov%2FBlast%2Ecgi%3FCMD%3DPut%26DATABASE%3Dnr%26ERROR%3DMessage%2BID%252329%2BError%253A%2BQuery%2Bstring%2Bnot%2Bfound%2Bin%2Bthe%2BCGI%2Bcontext%26EXPECT%3D1e%2D07%26HITLIST%5FSIZE%3D10%26MYNCBI%5FUSER%3D%2D1%26MYNCBI%5FUSER%3D%2D1%26PROGRAM%3Dblastx%26QUERY%3D%26USER%5FTYPE%3D0%26USER%5FTYPE%3D0"; title="Click to register for an account" +@@ -565,4 +564,4 @@ QBlastInfoEnd + <script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js"></script> + </body> + +-</html> +\ No newline at end of file ++</html> Modified: trunk/packages/python-biopython/trunk/debian/patches/series =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/series 2015-05-12 08:22:42 UTC (rev 19216) +++ trunk/packages/python-biopython/trunk/debian/patches/series 2015-05-12 09:30:16 UTC (rev 19217) @@ -1,2 +1,3 @@ remove_mathml-qname.patch fix_broken_test.patch +privacy_breach.patch Modified: trunk/packages/python-biopython/trunk/debian/rules =================================================================== --- trunk/packages/python-biopython/trunk/debian/rules 2015-05-12 08:22:42 UTC (rev 19216) +++ trunk/packages/python-biopython/trunk/debian/rules 2015-05-12 09:30:16 UTC (rev 19217) @@ -34,10 +34,6 @@ # This would not trigger a failure but bloats the build log with irrelevant noise EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2 -# The following test works only with python-rdflib (>= 4) -# If python-rdflib (>= 4) then do not exclude it - otherwise we exclude this test -EXCLUDERDFLIB=$(shell if dpkg --compare-versions `dpkg -l python-rdflib | grep ^ii | sed 's/ii *python-rdflib *\([-.0-9]\+\) *.*/\1/'` gt 4 ; then echo ""; else echo "Phylo_CDAO" ; fi) - # FIXME: These tests are failing for unknown reasons and this needs to be investigated # specifically since test_ColorSpiral and test_trie are running when called manually # . @@ -69,8 +65,7 @@ echo "***************************************************************************" else mkdir -p Tests_avoid - if [ "$(EXCLUDERDFLIB)" != "" ] ; then echo "You might like to install python-rdflib from experimental to run Phylo_CDAO test" ; else echo "Phylo_CDAO will be done"; fi - for avoid in $(EXCLUDEONLINE) $(EXCLUDENONFREE) $(EXCLUDENOTPACKAGED) $(EXCLUDEARCHamd64) $(EXCLUDEDATABASE) $(EXCLUDERDFLIB) $(EXCLUDEFAILINGTESTS) $(EXCLUDEPACKAGEINFLUX) \ + for avoid in $(EXCLUDEONLINE) $(EXCLUDENONFREE) $(EXCLUDENOTPACKAGED) $(EXCLUDEARCHamd64) $(EXCLUDEDATABASE) $(EXCLUDEFAILINGTESTS) $(EXCLUDEPACKAGEINFLUX) \ ; do \ mv Tests/test_$${avoid}.py Tests_avoid ; \ done _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
![http://www.ncbi.nlm.nih.gov/corehtml/query/MyNCBI/myncbihelpicon.gif"](http://www.ncbi.nlm.nih.gov/corehtml/query/MyNCBI/myncbihelpicon.gif"){kind=link}