35727 2003-12-13 07:41 0000 biopython-1.23.ebuild (update) 2003-12-30 18:47:51 0000 1 1 1 Unclassified Gentoo Linux Ebuilds unspecified All Linux RESOLVED TEST-REQUEST P2 enhancement --- 1 pbienst@gentoo.org george@gentoo.org pbienst@gentoo.org python@gentoo.org pbienst@gentoo.org 2003-12-13 07:41:42 0000 Ebuild for new version (also fixes a spelling error in the package description) Reproducible: Always Steps to Reproduce: 1. 2. 3. pbienst@gentoo.org 2003-12-13 07:42:23 0000 Created an attachment (id=22138) new ebuild liquidx@gentoo.org 2003-12-13 16:57:08 0000 throwing this to you george :) george@gentoo.org 2003-12-29 21:14:45 0000 Alastair: this should have gone to sci@... actually, now that we have a herd with working alias in place. Peter: First, no need to attach the ebuild when this is a trivial version bump. It is sufficient to rust drop a line that "I renamed the existing ebuild and it installed fine.." Or submit a patch of there were changes (in this case these were only decapitalisation of a few words in DESCRIPTION, so patch isn't even necessary). This makes it apparent what changes are necessary right away.. 2nd: Looks like setup.py got updated for this version in a scewy way. During src_install I am getting this (last few lines): byte-compiling /var/tmp/portage/biopython-1.23/image//usr/lib/python2.3/site-packages/Martel/RecordReader.py to RecordReader.pyc running install_data creating /usr/lib/python2.3/site-packages/Bio error: could not create '/usr/lib/python2.3/site-packages/Bio': Permission denied Note, I am running with userpriv usersandbox in FEATURES, so apparently this gets caught even before it gets to the "standard" sandbox. Could you please take a look at this? Looks like setup.py does not honor DESTDIR setting (at least not everywhere). You may try searching for "install_data" goal and do some seding.. It might work without usersandbox and usepriv, but this wasn't the case in 1.21, so it is better to fix this. George pbienst@gentoo.org 2003-12-30 02:07:54 0000 Sorry, I missed that because I had a /usr/lib/python2.2/site-packages/Bio directory around from a non-portage install of that package. Meanwhile I've discovered that there's a distutils eclass, so I've converted the ebuild to use it, which fixes the problem. pbienst@gentoo.org 2003-12-30 02:08:49 0000 Created an attachment (id=22838) biopython_1.21_1.23.diff george@gentoo.org 2003-12-30 18:47:51 0000 Ok, thats much better now :). I committed the ebuild, please test. George. 22138 2003-12-13 07:42 0000 new ebuild biopython-1.23.ebuild text/plain IyBDb3B5cmlnaHQgMTk5OS0yMDAzIEdlbnRvbyBUZWNobm9sb2dpZXMsIEluYy4KIyBEaXN0cmli dXRlZCB1bmRlciB0aGUgdGVybXMgb2YgdGhlIEdOVSBHZW5lcmFsIFB1YmxpYyBMaWNlbnNlIHYy CiMgJEhlYWRlcjogL2hvbWUvY3Zzcm9vdC9nZW50b28teDg2L2FwcC1zY2kvYmlvcHl0aG9uL2Jp b3B5dGhvbi0xLjIxLmVidWlsZCx2IDEuMyAyMDAzLzA5LzA4IDA3OjI0OjU4IG1zdGVycmV0IEV4 cCAkCgpJVVNFPSIiCgpTPSR7V09SS0RJUn0vJHtQfQpERVNDUklQVElPTj0iQmlvcHl0aG9uIC0g cHl0aG9uIG1vZHVsZXMgZm9yIGNvbXB1dGF0aW9uYWwgbW9sZWN1bGFyIGJpb2xvZ3kiClNSQ19V Ukk9Imh0dHA6Ly93d3cuYmlvcHl0aG9uLm9yZy9maWxlcy8ke1B9LnRhci5neiIKSE9NRVBBR0U9 Imh0dHA6Ly93d3cuYmlvcHl0aG9uLm9yZyIKCkRFUEVORD0iPj1kZXYtbGFuZy9weXRob24tMi4w CgkJPj1kZXYtcHl0aG9uL2VnZW5peC1teC1iYXNlLTIuMC4zCgkJPj1kZXYtcHl0aG9uL251bWVy aWMtMTkuMAoJCT49ZGV2LXB5dGhvbi9yZXBvcnRsYWItMS4xMSIKClNMT1Q9IjAiCkxJQ0VOU0U9 ImFzLWlzIgpLRVlXT1JEUz0ieDg2IH5wcGMgfnNwYXJjIH5hbHBoYSIKCnNyY19jb21waWxlKCkg ewoJcHl0aG9uIHNldHVwLnB5IGJ1aWxkIHx8IGRpZQojCXB5dGhvbiBzZXR1cC5weSB0ZXN0IC0t bm8tZ3VpIHx8IGRpZQp9CgpzcmNfaW5zdGFsbCgpIHsKCWVjaG8geSB8IHB5dGhvbiBzZXR1cC5w eSBpbnN0YWxsIC0tcHJlZml4PSR7RH0vdXNyIHx8IGRpZQoKCWRvZG9jIFBLRy1JTkZPIFJFQURN RSBORVdTIExJQ0VOU0UgQ09OVFJJQgoJZG9kb2MgRG9jLyogRG9jL2luc3RhbGwvKi50eHQKCWRv aHRtbCBEb2MvaW5zdGFsbC8qLmh0bWwKCWNwIC1yIERvYy9leGFtcGxlcy8gJHtEfS91c3Ivc2hh cmUvZG9jLyR7UEZ9Lwp9Cg== 22838 2003-12-30 02:08 0000 biopython_1.21_1.23.diff biopython_1.21_1.23.diff text/plain NGE1LDYKPiBpbmhlcml0IGRpc3R1dGlscwo+IAo3LDhjOQo8IFM9JHtXT1JLRElSfS8ke1B9Cjwg REVTQ1JJUFRJT049IkJpb3B5dGhvbiAtIHB5dGhvbiBtb2R1bGUgZm9yIENvbXB1dGF0aW9uYWwg TW9lbGN1bGFyIEJpb2xvZ3kiCi0tLQo+IERFU0NSSVBUSU9OPSJCaW9weXRob24gLSBQeXRob24g bW9kdWxlcyBmb3IgY29tcHV0YXRpb25hbCBtb2xlY3VsYXIgYmlvbG9neSIKMjIsMjNjMjMKPCAJ cHl0aG9uIHNldHVwLnB5IGJ1aWxkIHx8IGRpZQo8ICMJcHl0aG9uIHNldHVwLnB5IHRlc3QgLS1u by1ndWkgfHwgZGllCi0tLQo+IAlkaXN0dXRpbHNfc3JjX2NvbXBpbGUKMjcsMzBjMjcsMjgKPCAJ ZWNobyB5IHwgcHl0aG9uIHNldHVwLnB5IGluc3RhbGwgLS1wcmVmaXg9JHtEfS91c3IgfHwgZGll CjwgCjwgCWRvZG9jIFBLRy1JTkZPIFJFQURNRSBORVdTIExJQ0VOU0UgQ09OVFJJQgo8IAlkb2Rv YyBEb2MvKiBEb2MvaW5zdGFsbC8qLnR4dAotLS0KPiAJRE9DUz0iRG9jLyogRG9jL2luc3RhbGwv Ki50eHQiCj4gCWRpc3R1dGlsc19zcmNfaW5zdGFsbAo=