<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi Andreas,</div><div class="">Sascha and I had a look at -lsubunit the other day and he’s going to put in a patch. Its not needed in the gubbins or snp_sites build files, it appears to be an issue with the dependancies in check in Debian.</div><div class="">Regards,</div><div class="">Andrew</div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On 9 Dec 2015, at 16:36, Andreas Tille <<a href="mailto:tille@debian.org" class="">tille@debian.org</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Hi Andrew,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">I just uploaded the new version to Debian unstable. Please note that you somehow</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">missed to add -lsubunit to src/Makefile.am. I adapted the Debian patch for the</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">new version:</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""> </span><a href="https://anonscm.debian.org/cgit/debian-med/gubbins.git/tree/debian/patches/add_missing_lib_for_check.patch" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">https://anonscm.debian.org/cgit/debian-med/gubbins.git/tree/debian/patches/add_missing_lib_for_check.patch</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Thanks for your support</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""> Andreas.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">On Wed, Dec 09, 2015 at 03:57:41PM +0000, Andrew Page wrote:</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Hi,<br class="">I have pushed a fix for the build error on i386 as version 1.4.4<br class="">Details are here:<br class=""><a href="https://github.com/sanger-pathogens/gubbins/pull/158" class="">https://github.com/sanger-pathogens/gubbins/pull/158</a><span class="Apple-converted-space"> </span><<a href="https://github.com/sanger-pathogens/gubbins/pull/158" class="">https://github.com/sanger-pathogens/gubbins/pull/158</a>><br class=""><br class="">I replicated the bug on i386 and fixed it. The tests also pass on amd64 & OSX 10.10<br class=""><br class="">Regards,<br class="">Andrew<br class=""><br class=""><br class=""><blockquote type="cite" class="">On 6 Dec 2015, at 06:40, Andreas Tille <<a href="mailto:andreas@an3as.eu" class="">andreas@an3as.eu</a>> wrote:<br class=""><br class="">Hi Andrew,<br class=""><br class="">I hereby forward a build issue on i386 architecture.<br class=""><br class="">Kind regards<br class=""><br class=""> Andreas.<br class=""><br class="">On Sat, Dec 05, 2015 at 10:30:32PM -0500, Aaron M. Ucko wrote:<br class=""><blockquote type="cite" class="">Source: gubbins<br class="">Version: 1.4.3-1<br class="">Severity: important<br class="">Justification: fails to build from source<br class=""><br class="">The i386 build of gubbins failed:<br class=""><br class="">FAIL: run_all_tests<br class="">============================================================================<br class="">Testsuite summary for gubbins 1.4.3<br class="">============================================================================<br class=""># TOTAL: 1<br class=""># PASS: 0<br class=""># SKIP: 0<br class=""># XFAIL: 0<br class=""># FAIL: 1<br class=""># XPASS: 0<br class=""># ERROR: 0<br class="">============================================================================<br class="">See src/test-suite.log<br class=""><br class="">I was able to reproduce the error in an i386 chroot, yielding the following<br class="">details:<br class=""><br class="">FAIL: run_all_tests<br class="">===================<br class=""><br class="">Running suite(s): Creating_SNP_Sites<br class=""> Parsing a phylip file<br class=""> Parsing a vcf file<br class=""> checking branch sequences<br class=""> Checking the gubbins functionality<br class=""> snp_searching<br class="">94%: Checks: 39, Failures: 2, Errors: 0<br class="">../tests/check_snp_sites.c:73:F:snp_sites:valid_alignment_with_multiple_lines_per_sequence:0: Invalid ALN file for multiple lines per seq<br class="">../tests/check_snp_sites.c:85:F:snp_sites:two_sequences:0: Invalid ALN file for multiple lines per seq<br class="">FAIL run_all_tests (exit status: 1)<br class=""><br class="">Could you please take a look?<br class=""><br class="">Thanks!<br class=""><br class="">_______________________________________________<br class="">Debian-med-packaging mailing list<br class=""><a href="mailto:Debian-med-packaging@lists.alioth.debian.org" class="">Debian-med-packaging@lists.alioth.debian.org</a><br class="">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging<br class=""><br class=""></blockquote><br class="">--<span class="Apple-converted-space"> </span><br class=""><a href="http://fam-tille.de" class="">http://fam-tille.de</a><br class=""></blockquote><br class=""><br class=""><br class=""><br class="">--<span class="Apple-converted-space"> </span><br class="">The Wellcome Trust Sanger Institute is operated by Genome Research<span class="Apple-converted-space"> </span><br class="">Limited, a charity registered in England with number 1021457 and a<span class="Apple-converted-space"> </span><br class="">company registered in England with number 2742969, whose registered<span class="Apple-converted-space"> </span><br class="">office is 215 Euston Road, London, NW1 2BE.<span class="Apple-converted-space"> </span><br class=""><br class=""><br class=""></blockquote><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">--<span class="Apple-converted-space"> </span></span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://fam-tille.de/" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">http://fam-tille.de</a></div></blockquote></div><br class="">
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The Wellcome Trust Sanger Institute is operated by Genome Research
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