Created attachment 297007 [details] GBrowse-2.44.ebuild which uses the patches of Martin Mokrejš 'emerge GBrowse' fails with: ... >>> Installing (1 of 1) sci-biology/GBrowse-2.44 * checking 536 files for package collisions * This package will overwrite one or more files that may belong to other * packages (see list below). You can use a command such as `portageq * owners / <filename>` to identify the installed package that owns a * file. If portageq reports that only one package owns a file then do * NOT file a bug report. A bug report is only useful if it identifies at * least two or more packages that are known to install the same file(s). * If a collision occurs and you can not explain where the file came from * then you should simply ignore the collision since there is not enough * information to determine if a real problem exists. Please do NOT file * a bug report at http://bugs.gentoo.org unless you report exactly which * two packages install the same file(s). Once again, please do NOT file * a bug report unless you have completely understood the above message. * * Detected file collision(s): * * /var/db/gbrowse2/databases/gbrowse_syn/rice/rice.gff3 * /var/db/gbrowse2/databases/gbrowse_syn/alignments/rice.aln.gz ... * /usr/share/man/man1/gtf2gff3.pl.1.bz2 * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * sci-biology/GBrowse-2.39 * /usr/bin/bed2gff3.pl * /usr/bin/gbrowse_change_passwd.pl ... * /var/db/gbrowse2/databases/yeast_scaffolds/chromosomes.gff3 * * Package 'sci-biology/GBrowse-2.44' NOT merged due to file collisions. * If necessary, refer to your elog messages for the whole content of the * above message. >>> Failed to install sci-biology/GBrowse-2.44, Log file: It is almost the same problem as described in Bug 347165 gbrowse-2.03 fails to update from 2.00 because of file collision Bug 356211 gbrowse fails to update to version 2.26 if gbrowse-2.03 is installed Bug 366975 gbrowse-2.33 fails to install, due to ACCESS VIOLATION I tried to adapt the patches of Martin Mokrejš (Comment 5 of Bug 366975) to GBrowse-2.44, but it did not help
Created attachment 297009 [details] destdir.patch
Created attachment 297011 [details] gbrowse_metadb_config.pl.patch
Created attachment 297013 [details] /var/tmp/portage/sci-biology/GBrowse-2.44/temp/build.log
Wow, four open bug reports about essentially the same problem. Should this package be SLOTted at all, or is this caused by a lack of maintenance?
Yep, definitely a bug that I've neglected. Looking at it, thanks for the reports. Feel free to touch the ebuilds (I'm starved for time).
Disabled webapp autoslotting in GBrowse-2.44-r1, thank you for reporting. Rejecting the patches, since they are not relevant to the collisions and don't fix them, and should be sent upstream.
Few comments to the official GBrowse ebuild. Although the install process says: * Messages for package sci-biology/GBrowse-2.44-r1: * (server owned) /var/tmp/gbrowse2 * (server owned) /var/db/gbrowse2 * (server owned) /var/db/gbrowse2/sessions * (server owned) /var/db/gbrowse2/userdata I get in the end: # ls -la /var/tmp/gbrowse2 /var/db/gbrowse2 /var/db/gbrowse2/sessions /var/db/gbrowse2/userdata ls: cannot access /var/db/gbrowse2/sessions: No such file or directory ls: cannot access /var/db/gbrowse2/userdata: No such file or directory /var/db/gbrowse2: total 20 drwxr-xr-x 3 apache apache 4096 Oct 1 11:50 . drwxr-xr-x 6 root root 4096 Jan 8 01:54 .. drwxr-xr-x 8 apache apache 4096 Jan 8 01:54 databases -rw-r----- 1 apache apache 12288 Aug 1 20:06 sessions.db -rw-r--r-- 1 apache apache 0 Aug 1 20:06 sessions.db.lck /var/tmp/gbrowse2: total 76 drwxr-xr-x 3 apache apache 4096 Jan 8 01:36 . drwxrwxrwt 9 root root 65536 Jan 7 15:18 .. drwxr-xr-x 11 apache apache 4096 Jan 8 01:49 locks # Andrey, please pre-create the two missing directories manually. Second, because you relocate the package under GBrowse (instead of gbrowse2 in original install process) I get: [Sun Jan 08 02:03:39 2012] [error] [client 127.0.0.1] File does not exist: /var/www/localhost/htdocs/gbrowse2, referer: http://127.0.0.1/cgi-bin/gbrowse/pop_demo/ Please make a symlink gbrowse2 -> GBrowse or fix the /etc/gbrowse2/GBrowse.conf file (rewrite /var/lib/gbrowse2 to /var/db/gbrowse2). [Sun Jan 08 02:08:59 2012] [error] [client 127.0.0.1] File does not exist: /var/www/localhost/htdocs/gbrowse2/i/pop_demo, referer: http://127.0.0.1/cgi-bin/gbrowse/pop_demo/ I had these tricks in the science overlay under sci-biology/gbrowse (and maybe there are more needed to be transferred): ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/var/www/localhost/htdocs/gbrowse2/i || die einfo "Probably you want to install a cron job to remove the generated temporary images:" einfo "find /var/tmp/gbrowse2/images -type f -atime +20 -print -exec rm {}" And, neither the PNG export nor FASTA export does work for me from the pop_demo at least (in the menu File/Export as).
And the /var/db/gbrowse2 should be *recursively* assigned to apache.apache. I know, this should be done by the server_owned but that is what we talked about months ago: it just does not work. That is why my gbrowse ebuild in overlay seemed ugly, but it worked. ;) Test with http://127.0.0.1/cgi-bin/gbrowse/yeast/ and if you see in error_log: [Sun Jan 08 02:45:17 2012] [error] [client 127.0.0.1] Can't open sequence index file /var/db/gbrowse2/databases/yeast_scaffolds/directory.index: No such file or directory at /usr/lib/perl5/vendor_perl/5.12.4/Bio/DB/Fasta.pm line 527., referer: http://127.0.0.1/cgi-bin/gbrowse/yeast/ After the owner or perms changes the file will be created automagically by gbrowse with apache.apache ownership on the fly.
dev-perl/TermReadKey should be added to RDEPEND (needed by gbrowse_metadb_config.pl at least)
