{"action":"created","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/33","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/33/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/33/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/33/events","html_url":"https://github.com/cjfields/redmine-test/issues/33","id":107444411,"number":33,"title":"bioperl-ext: make test fails using io_lib v. 1.9 or higher","user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Category:%20bioperl-ext","name":"Category: bioperl-ext","color":"000099"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Priority:%20Normal","name":"Priority: Normal","color":"666600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Status:%20New","name":"Status: New","color":"FF6600"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/cjfields/redmine-test/milestones/1","html_url":"https://github.com/cjfields/redmine-test/milestones/main-trunk","labels_url":"https://api.github.com/repos/cjfields/redmine-test/milestones/1/labels","id":1315666,"number":1,"title":"main-trunk","description":null,"creator":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"open_issues":9,"closed_issues":0,"state":"open","created_at":"2015-09-21T04:19:26Z","updated_at":"2015-09-21T04:54:22Z","due_on":null,"closed_at":null},"comments":17,"created_at":"2015-09-21T04:54:22Z","updated_at":"2015-09-21T04:55:18Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Martin Mokrejs** (Martin Mokrejs)\nOriginal Redmine Issue: 2074, https://redmine.open-bio.org/issues/2074\nOriginal Date: 2006-08-12\nOriginal Assignee: Bioperl Guts\n\n---\n\nI tried to compile current bioperl-ext from CVS against io\\_lib-1.9.0 and surprisingly succeeded. ;-) But the make test fails with:\n\n$ make test\nmake[1]: Entering directory \\`/home/mmokrejs/proj/bioperl/bioperl-ext/Bio/Ext/Align’\nmake[1]: Leaving directory \\`/home/mmokrejs/proj/bioperl/bioperl-ext/Bio/Ext/Align’\nmake[1]: Entering directory \\`/home/mmokrejs/proj/bioperl/bioperl-ext/Bio/SeqIO/staden’\nmake[1]: Leaving directory \\`/home/mmokrejs/proj/bioperl/bioperl-ext/Bio/SeqIO/staden’\nPERL\\_DL\\_NONLAZY=1 /usr/bin/perl5.8.8 “-MExtUtils::Command::MM” “-e” “test\\_harness(0, ‘blib/lib’, ‘blib/arch’)” t/\\*.t\nt/basic….ok\nAll tests successful.\nFiles=1, Tests=1, 0 wallclock secs ( 0.03 cusr + 0.02 csys = 0.05 CPU)\nmake[1]: Entering directory \\`/home/mmokrejs/proj/bioperl/bioperl-ext/Bio/Ext/Align’\nPERL\\_DL\\_NONLAZY=1 /usr/bin/perl5.8.8 “-I../blib/lib” “-I../blib/arch” test.pl\n1..9\n\n1.  Running under perl version 5.008008 for linux\n2.  Current time local: Sat Aug 12 20:01:43 2006\n3.  Current time GMT: Sat Aug 12 18:01:43 2006\n4.  Using Test.pm version 1.25\n    ok 1\n    ok 2\n    ok 3\n    ok 4\n    ProteinSW Matrix calculation: [ 0] Cells 0%\n    ok 5\n    ok 6\n    ok 7\n    ok 8\n\n——————- EXCEPTION ——————-\nMSG: Algorithm must be either 1 or 2\nSTACK Bio::Tools::dpAlign::new /usr/lib/perl5/vendor\\_perl/5.8.8/Bio/Tools/dpAlign.pm:286\nSTACK toplevel test.pl:96\n\n------------------------------------------------------------------------\n\nmake[1]: ****\\* [test\\_dynamic] Error 255\nmake[1]: Leaving directory \\`/home/mmokrejs/proj/bioperl/bioperl-ext/Bio/Ext/Align’\nmake[1]: Entering directory \\`/home/mmokrejs/proj/bioperl/bioperl-ext/Bio/SeqIO/staden’\nPERL\\_DL\\_NONLAZY=1 /usr/bin/perl5.8.8 “-MExtUtils::Command::MM” “-e” “test\\_harness(0, ‘../blib/lib’, ‘../blib/arch’)” test.pl\ntest….dubious\n Test returned status 0 (wstat 8, 0x8)\nDIED. FAILED tests 3-94\n Failed 92/94 tests, 2.13% okay\nFailed Test Stat Wstat Total Fail List of Failed\n———————————————————————————————————————-\ntest.pl 0 8 94 184 3-94\nFailed 1/1 test scripts. 92/94 subtests failed.\nFiles=1, Tests=94, 0 wallclock secs ( 0.28 cusr + 0.04 csys = 0.32 CPU)\nFailed 1/1 test programs. 92/94 subtests failed.\nmake[1]: ****\\* [test\\_dynamic] Error 255\nmake[1]: Leaving directory \\`/home/mmokrejs/proj/bioperl/bioperl-ext/Bio/SeqIO/staden’\n$\n\n\n\n\n"},"comment":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/comments/141877901","html_url":"https://github.com/cjfields/redmine-test/issues/33#issuecomment-141877901","issue_url":"https://api.github.com/repos/cjfields/redmine-test/issues/33","id":141877901,"user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"created_at":"2015-09-21T04:55:18Z","updated_at":"2015-09-21T04:55:18Z","body":"---\n\nOriginal Redmine Comment\nAuthor Name: **Chris Fields** (Chris Fields)\nOriginal Date: 2007-10-23T17:54:41Z\n\n---\n\nThere was no XSUB declared in the last patch for read\\_staden\\_graph. I added a quick one in (the args are exactly the same as for staden\\_read\\_trace(), so it is a copy-paste job). So far everything works, though I did get a warning on make:\n\nread.xs: In function ‘staden\\_read\\_graph’:\nread.xs:200: warning: passing argument 2 of ‘Perl\\_newRV’ from incompatible pointer type\nread.xs:201: warning: passing argument 2 of ‘Perl\\_newRV’ from incompatible pointer type\nread.xs:202: warning: passing argument 2 of ‘Perl\\_newRV’ from incompatible pointer type\nread.xs:203: warning: passing argument 2 of ‘Perl\\_newRV’ from incompatible pointer type\nread.xs:204: warning: passing argument 2 of ‘Perl\\_newRV’ from incompatible pointer type\nRunning Mkbootstrap for Bio::SeqIO::staden::read ()\n\nRunning the test script in bug 2329 works, though we might want to delve into the above warning some more.\n\n"}}