* package sci-chemistry/refmac-5.5.0110-r2 NOT merged * * Detected file collision(s): * * /usr/bin/libcheck * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * sci-chemistry/makecif-5.6.6 * /usr/bin/libcheck * Starting tests ... [REFMAC5] TLS refinement with 4 molecules (1VK8 INFL example.) ... FAIL [REFMAC5] sad refinement (2ISB INFL example.) ... FAIL [REFMAC5] twinned refinement (1VR7 example.) ... FAIL ====================================================================== FAIL: [REFMAC5] TLS refinement with 4 molecules (1VK8 INFL example.) ---------------------------------------------------------------------- Traceback (most recent call last): File "/var/tmp/portage/sci-chemistry/refmac-5.5.0110-r2/work/test-framework/refmac5/test_refmac5.py", line 154, in test_4_domain_tls self.assertEqual(status, 0) AssertionError: 1 != 0 ====================================================================== FAIL: [REFMAC5] sad refinement (2ISB INFL example.) ---------------------------------------------------------------------- Traceback (most recent call last): File "/var/tmp/portage/sci-chemistry/refmac-5.5.0110-r2/work/test-framework/refmac5/test_refmac5.py", line 199, in test_sad_refinement self.assertEqual(status, 0) AssertionError: 1 != 0 ====================================================================== FAIL: [REFMAC5] twinned refinement (1VR7 example.) ---------------------------------------------------------------------- Traceback (most recent call last): File "/var/tmp/portage/sci-chemistry/refmac-5.5.0110-r2/work/test-framework/refmac5/test_refmac5.py", line 105, in test_twinned_refinement self.assertEqual(status, 0) AssertionError: 1 != 0 ---------------------------------------------------------------------- Ran 3 tests in 0.022s FAILED (failures=3) * ERROR: sci-chemistry/refmac-5.5.0110-r2 failed: Reproducible: Always
Created attachment 258035 [details] /var/log/portage/sci-chemistry:refmac-5.5.0110-r2:20101225-184014.log
Created attachment 258036 [details] emerge --info
+ 25 Dec 2010; Justin Lecher <jlec@gentoo.org> refmac-5.5.0110-r2.ebuild: + Removed installation of libcheck again, #349700 + Please sync and try again the test. There must be three extra log in the tempdir. Could you attach them please.
Archtested on x86: Everything fine Do you still want the logs?
No thanks. That was just in case it isn't resolved.
I still get the test failures. And these are the first three tests and you are running with -j3. I'll bet a beer that you get 4 test failures with -j4. If you still wan't these logs, tell me where I find them in the tempdir.
(In reply to comment #6) > I still get the test failures. And these are the first three tests and you are > running with -j3. I'll bet a beer that you get 4 test failures with -j4. > > If you still wan't these logs, tell me where I find them in the tempdir. > There are only three tests which all fail. You find the log files in /var/tmp/portage/sci-chemistry/refmac-5.5.0110-r2/temp/.
> There are only three tests which all fail. You find the log files in > /var/tmp/portage/sci-chemistry/refmac-5.5.0110-r2/temp/. > All test logs log exactly like this: # cat test_twinned_refinement.log >>>>>> CCP4 library signal ccp4_general:Cannot open environ.def (Error) raised in ccp4fyp <<<<<< refmac5: Cannot open environ.def refmac5: Cannot open environ.def Times: User: 0.0s System: 0.0s Elapsed: 0:00
(In reply to comment #8) > > There are only three tests which all fail. You find the log files in > > /var/tmp/portage/sci-chemistry/refmac-5.5.0110-r2/temp/. > > > > All test logs log exactly like this: > > # cat test_twinned_refinement.log > >>>>>> CCP4 library signal ccp4_general:Cannot open environ.def (Error) > raised in ccp4fyp <<<<<< > refmac5: Cannot open environ.def > refmac5: Cannot open environ.def > Times: User: 0.0s System: 0.0s Elapsed: 0:00 > I just setuped a fresh system and will test it. If the testsuite is not working I will remove it again. I took it from the upstream monolithic package, where it is supposed to be run with a whole bunch of tests.
I found it. Please prceed with bug 350233 which should fix this one.
I'm sorry, it's still exaclty the same.
(In reply to comment #11) > I'm sorry, it's still exaclty the same. > PLease check whether you have /usr/share/ccp4/include/environ.def. And add the output of env | grep CCP4, thanks.
(In reply to comment #12) > (In reply to comment #11) > > I'm sorry, it's still exaclty the same. > > > > PLease check whether you have /usr/share/ccp4/include/environ.def. # equery b /usr/share/ccp4/include/environ.def * Searching for /usr/share/ccp4/include/environ.def ... sci-libs/ccp4-libs-6.1.3-r5 (/usr/share/ccp4/include/environ.def) > And add the output of env | grep CCP4, thanks. empty string
Mmmh, I really don't understand what is going on there. I will test it myself, again.
+*ccp4-libs-6.1.3-r7 (10 Jan 2011) + + 10 Jan 2011; Justin Lecher <jlec@gentoo.org> -ccp4-libs-6.1.3-r4.ebuild, + +ccp4-libs-6.1.3-r7.ebuild: + Moved the installation of profile files from sci-chemistry/ccp4-apps to + sci-libs/ccp4-libs, #349700 + Should work now. For sure :)
Please close if it is working.
Tried sci-chemistry/refmac-5.5.0110-r2 with ccp4-libs-6.1.3-r7, still the same. :(
(In reply to comment #17) > Tried sci-chemistry/refmac-5.5.0110-r2 with ccp4-libs-6.1.3-r7, still the same. > :( > Could please attach the output of env and the environmental file?
I found the error. If you are emerging ccp4-libs and refmac in a row, /etc/profile doesn't get sourced and so some env stuff is missing. I forced the sourcing before test, which should fix all that now.
It is fixed now. Thanks!
