For some reason webapp-config tries to delete a path to be created (I don't think it is wise at all, btw). Anyway, it dies because os.rmdir() fails. However, after the package installs one can see the soflink did exist. Yeah, maybe that is just os.rmdir() vs. os.unlink() issue. The sci-biology/gbrowse is now being moved to main tree from science overlay. >>> Completed installing gbrowse-2.39 into /var/tmp/portage/sci-biology/gbrowse-2.39/image/ ecompressdir: bzip2 -9 /usr/share/man >>> Installing (1 of 1) sci-biology/gbrowse-2.39 * vhosts USE flag not set - auto-installing using webapp-config * This is an installation * gbrowse-2.39 is not installed - using install mode * Running /usr/sbin/webapp-config -I -h localhost -u root -d /gbrowse gbrowse 2.39 * Creating required directories * Linking in required files * This can take several minutes for larger apps Traceback (most recent call last): File "/usr/sbin/webapp-config-2.7", line 44, in <module> main() File "/usr/sbin/webapp-config-2.7", line 41, in main config.run() File "/usr/lib/python2.7/site-packages/WebappConfig/config.py", line 1190, in run self.config.get('USER', 'pvr')).install() File "/usr/lib/python2.7/site-packages/WebappConfig/server.py", line 237, in install self.__add.mkdirs() File "/usr/lib/python2.7/site-packages/WebappConfig/worker.py", line 335, in mkdirs self.mkfile(directory + '/' + i) File "/usr/lib/python2.7/site-packages/WebappConfig/worker.py", line 451, in mkfile os.rmdir(dst_name) OSError: [Errno 20] Not a directory: '/var/www/localhost/htdocs/gbrowse//i' * Running /usr/sbin/webapp-cleaner -p -C /gbrowse * Unused versions of /gbrowse detected. * To clean, run the following command: * emerge -Cav =gbrowse-2.39 * Please run gbrowse_metadb_config.pl to update SQLite flatfiles of the live database. >>> Recording sci-biology/gbrowse in "world" favorites file... * Messages for package sci-biology/gbrowse-2.39: * (info) /var/tmp/portage/sci-biology/gbrowse-2.39/work/GBrowse-2.39/INSTALL (lang: en) * vhosts USE flag not set - auto-installing using webapp-config * This is an installation * gbrowse-2.39 is not installed - using install mode * Running /usr/sbin/webapp-config -I -h localhost -u root -d /gbrowse gbrowse 2.39 >>> Auto-cleaning packages... >>> No outdated packages were found on your system. * GNU info directory index is up-to-date. vrapenec ~ # ls -la /var/www/localhost/htdocs/gbrowse/ total 192 drwxr-xr-x 9 root root 4096 Jul 30 21:00 . drwxr-xr-x 12 apache root 4096 Jul 30 21:00 .. -r--r--r-- 2 root root 36588 Jul 30 21:00 annotation_help.html drwxr-xr-x 2 root root 4096 Jul 30 21:00 cgi-bin drwxr-xr-x 3 root root 4096 Jul 30 21:00 css drwxr-xr-x 3 root root 4096 Jul 30 21:00 etc drwxr-xr-x 2 root root 4096 Jul 30 21:00 example_scripts -r--r--r-- 2 root root 69981 Jul 30 21:00 gbrowse_karyotype_help.html -r--r--r-- 2 root root 5940 Jul 30 21:00 gbrowse_syn_help.html -r--r--r-- 2 root root 20168 Jul 30 21:00 general_help.html -r--r--r-- 2 root root 7865 Jul 30 21:00 general_help.html.zh -r--r--r-- 2 root root 5289 Jul 30 21:00 gmod_cog.jpeg lrwxrwxrwx 1 root root 24 Jul 30 21:00 i -> /var/tmp/gbrowse2/images drwxr-xr-x 7 root root 4096 Jul 30 21:00 images drwxr-xr-x 2 root root 4096 Jul 30 21:00 js drwxr-xr-x 7 root root 4096 Jul 30 21:00 tutorial vrapenec ~ #
I'm trying to take care of webapp-config these days, but I'm strapped for time. Do you think you can produce a patch?
(In reply to comment #1) > I'm trying to take care of webapp-config these days, but I'm strapped for > time. Do you think you can produce a patch? Bug is no longer relevant. It was either fixed on it's own, or a patch was added but this doesn't affect either GBrowse-2.48 or GBrowse-2.44-r1 on portage tree using the latest webapp-config from HEAD^.
Closing this as OBSOLETE, feel free to reopen if this issue happens again