[task #3781] Describe the test-suite vs. sample script usage differences in the manual.

URL: http://gna.org/task/?3781 Summary: Describe the test-suite vs. sample script usage differences in the manual. Project: relax Submitted by: bugman Submitted on: Thursday 09/28/2006 at 17:03 Should Start On: Thursday

[bug #7226] Test Suite Check: modsel.py (failure in the reading of model m0 results!)

Update of bug #7226 (project relax): Status: Confirmed = Fixed Assigned to:None = bugman Open/Closed:Open = Closed Summary: Test

[bug #7277] palmer.py Stage 2 error

Update of bug #7277 (project relax): Status: Need Info = Confirmed Assigned to:None = bugman ___ Reply to this item at:

[bug #7296] Potential full analysis read problem

Update of bug #7296 (project relax): Status: Need Info = Works For Me Open/Closed:Open = Closed ___ Follow-up Comment #2: This bug has been

[bug #7277] palmer.py Stage 2 error (mfout reading error)

Update of bug #7277 (project relax): Status: Confirmed = Fixed Open/Closed:Open = Closed Summary: palmer.py Stage 2 error = palmer.py Stage 2 error (mfout reading error)

[bug #7333] Failure of the PDB related functions.

URL: http://gna.org/bugs/?7333 Summary: Failure of the PDB related functions. Project: relax Submitted by: bugman Submitted on: Saturday 10/07/2006 at 17:00 Category: None Priority: 5 - Normal

[bug #7333] Failure of the PDB related functions.

Update of bug #7333 (project relax): Status:None = Fixed Open/Closed:Open = Closed ___ Follow-up Comment #1: This bug was fixed in

[bug #7335] AttributeError: PDB instance has no attribute 'heteronuc'

Update of bug #7335 (project relax): Status:None = Fixed Open/Closed:Open = Closed ___ Follow-up Comment #1: This was fixed in

[bug #7336] PDB failure: RelaxError: The residue number argument None must be an integer.

Update of bug #7336 (project relax): Status:None = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[task #3629] Fix the threading code.

Update of task #3629 (project relax): Percent Complete: 0% = 100% Open/Closed:Open = Closed Summary: Remove the dependence on Popen3 in the threading code. = Fix the threading code.

[task #3629] Fix the threading code.

Update of task #3629 (project relax): Percent Complete:100% = 0% ___ Reply to this item at: http://gna.org/task/?3629 ___ Message sent

[task #3629] Fix the threading code.

Update of task #3629 (project relax): Open/Closed: Closed = Open ___ Reply to this item at: http://gna.org/task/?3629 ___ Message sent

[bug #7241] Problem with reading RNA PDBs

Follow-up Comment #2, bug #7241 (project relax): This bug hadn't been completely fixed. The function for reading the sequence from the Scientific Python PDB data structure was accessing solely 'peptide_chains'! The fix to the 1.2 line is described at

[task #3930] Create the GNU/Linux development platform web page

Update of task #3930 (project relax): Category:None = Web pages (HTML) ___ Reply to this item at: http://gna.org/task/?3930 ___ Message sent

[bug #6874] math domain error (in MS Windows).

Update of bug #6874 (project relax): Status:None = Wont Fix Assigned to:None = bugman Open/Closed:Open = Closed

[task #4002] Implement grace.write() in reduced spectral density mapping.

URL: http://gna.org/task/?4002 Summary: Implement grace.write() in reduced spectral density mapping. Project: relax Submitted by: bugman Submitted on: Sunday 10/22/2006 at 03:39 Should Start On: Sunday 10/22/2006 at 00:00

[bug #7540] self.relax.generic.pdb.load() doesn't exist!

Update of bug #7540 (project relax): Severity: 2 - Minor = 4 - Important Assigned to:None = bugman Summary: pdb.load() doesn't exist (?) = self.relax.generic.pdb.load() doesn't exist!

[bug #7540] self.relax.generic.pdb.load() doesn't exist!

Update of bug #7540 (project relax): Status:None = Ready For Test ___ Follow-up Comment #1: This problem was originally reported at

[bug #7540] self.relax.generic.pdb.load() doesn't exist!

Update of bug #7540 (project relax): Status: Ready For Test = Fixed Open/Closed:Open = Closed ___ Follow-up Comment #2: This bug was confirmed

[task #4002] Implement grace.write() in reduced spectral density mapping.

Follow-up Comment #1, task #4002 (project relax): Daniel Perez confirmed that this new code now is fully functional in the post https://mail.gna.org/public/relax-devel/2006-10/msg00154.html (Message-id: [EMAIL PROTECTED]). ___ Reply to

[bug #7583] No relaxation data is read if the file contains more than 4 columns.

Update of bug #7583 (project relax): Status: In Progress = Fixed Open/Closed:Open = Closed ___ Follow-up Comment #1: This bug was fixed in

[bug #7583] No relaxation data is read if the file contains more than 4 columns.

Follow-up Comment #2, bug #7583 (project relax): The issue was that lines were being skipped if there wasn't exactly 4 columns! ___ Reply to this item at: http://gna.org/bugs/?7583 ___

[bug #7587] Failure in the reading of the model-free results files from 1.2.4 relax versions and earlier.

Update of bug #7587 (project relax): Status: In Progress = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #7587] Failure in the reading of the model-free results files from 1.2.4 relax versions and earlier.

Update of bug #7587 (project relax): Status:None = In Progress Assigned to:None = bugman ___ Follow-up Comment #1: The RelaxFault was

[bug #7616] Incorrect model selection of the global model if the local tm models are included.

URL: http://gna.org/bugs/?7616 Summary: Incorrect model selection of the global model if the local tm models are included. Project: relax Submitted by: bugman Submitted on: Saturday 11/04/2006 at 06:05 Category: relax's

[bug #7616] Incorrect model selection of the global model if the local tm models are included.

Follow-up Comment #1, bug #7616 (project relax): This bug was introduced in r2516 (https://mail.gna.org/public/relax-commits/2006-07/msg00010.html). ___ Reply to this item at: http://gna.org/bugs/?7616

[bug #7616] Incorrect model selection of the global model if the local tm models are included.

Update of bug #7616 (project relax): Status:None = Fixed Open/Closed:Open = Closed ___ Follow-up Comment #2: relax versions 1.2.5

[bug #7645] No attribute heteronuc

Update of bug #7645 (project relax): Status:None = In Progress Assigned to:None = bugman ___ Reply to this item at:

[bug #7677] Failure of profiling due to the relax function 'print_stats()'.

be due to a newer version of the standard Python profile code. ___ Follow-up Comments: --- Date: Thursday 11/09/2006 at 03:05 By: Edward d Auvergne Edward d Auvergne Profiling, which

[bug #7677] Failure of profiling due to the relax function 'print_stats()'.

Update of bug #7677 (project relax): Status: In Progress = Fixed Open/Closed:Open = Closed ___ Follow-up Comment #1: The fix was simply to

[bug #7678] MS Windows failure of the 'source_dist' SCons target.

11/09/2006 at 06:22 By: Edward d Auvergne Edward d Auvergne When running the 'source_dist' SCons target on MS Windows, the target fails with the following error message: ### # Cleaning up # ### Removing the files ending in ['so', 'sconsign', 'dll']. scons: *** [clean

[task #4106] List the relax distribution packages for all versions on the download page.

: --- Date: Thursday 11/09/2006 at 06:44 By: Edward d Auvergne Edward d Auvergne On the webpage http://nmr-relax.com/download.html, the 'Old releases' section could be modified to include a table of all the distribution packages at location http://download.gna.org/relax. This could be in the format

[bug #7641] Infinite chi-squared RelaxError when the chi-squared value is zero.

Update of bug #7641 (project relax): Status:None = Fixed Open/Closed:Open = Closed ___ Follow-up Comment #2: This was fixed by Gary

[bug #7875] Script full_analysis.py shoots error when starting monte carlo simulations for the final run

Update of bug #7875 (project relax): Status:None = Confirmed Assigned to:None = bugman Operating System: GNU/Linux = All systems

[bug #7875] Script full_analysis.py shoots error when starting monte carlo simulations for the final run

Follow-up Comment #2, bug #7875 (project relax): Actually the cause of this bug is different to that of bug #7226 (https://gna.org/bugs/?7226). The reason is because the 'model_selection()' user function is incorrectly copying the data into the model selection run when the local tm global

[bug #7875] Script full_analysis.py shoots error when starting monte carlo simulations for the final run

Update of bug #7875 (project relax): Status: Confirmed = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #7755] modsel.py error with eliminate

Update of bug #7755 (project relax): Status: Confirmed = Fixed Assigned to:None = bugman Open/Closed:Open = Closed

[bug #7890] Monte Carlo simulation state is on after reading a results file containing sims.

Update of bug #7890 (project relax): Status:None = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #7891] The heteronuc data structure does not exist after reading reading model-free results files.

URL: http://gna.org/bugs/?7891 Summary: The heteronuc data structure does not exist after reading reading model-free results files. Project: relax Submitted by: bugman Submitted on: Thursday 11/30/2006 at 09:45 Category:

[bug #7891] The heteronuc data structure does not exist after reading reading model-free results files.

Update of bug #7891 (project relax): Status:None = Fixed Assigned to:None = bugman Open/Closed:Open = Closed

[bug #7970] Problems with the Molmol macros for fast correlation times.

URL: http://gna.org/bugs/?7970 Summary: Problems with the Molmol macros for fast correlation times. Project: relax Submitted by: bugman Submitted on: Saturday 12/09/2006 at 01:06 Category: relax's source code

[bug #7970] Problems with the Molmol macros for fast correlation times.

Update of bug #7970 (project relax): Status:None = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #7979] Problems with the diffusion tensor PDB representation user function with MC sims.

URL: http://gna.org/bugs/?7979 Summary: Problems with the diffusion tensor PDB representation user function with MC sims. Project: relax Submitted by: bugman Submitted on: Sunday 12/10/2006 at 02:20 Category: relax's

[bug #8059] RelaxFault in eliminate()

Update of bug #8059 (project relax): Assigned to:None = bugman ___ Reply to this item at: http://gna.org/bugs/?8059 ___ Message sent

[bug #8182] Failure of the docstring fetching Scons target.

URL: http://gna.org/bugs/?8182 Summary: Failure of the docstring fetching Scons target. Project: relax Submitted by: bugman Submitted on: Saturday 01/06/2007 at 03:24 Category: Scons build system

[bug #8183] Test suite failure of the test labelled 'S2 difference stored in a new run'.

URL: http://gna.org/bugs/?8183 Summary: Test suite failure of the test labelled 'S2 difference stored in a new run'. Project: relax Submitted by: bugman Submitted on: Saturday 01/06/2007 at 04:05 Category: relax's source

[bug #8183] Test suite failure of the test labelled 'S2 difference stored in a new run'.

Update of bug #8183 (project relax): Status:None = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #8187] More problems with the 'heteronuc' attribute.

URL: http://gna.org/bugs/?8187 Summary: More problems with the 'heteronuc' attribute. Project: relax Submitted by: bugman Submitted on: Saturday 01/06/2007 at 09:44 Category: relax's source code Severity:

[bug #8187] More problems with the 'heteronuc' attribute.

Update of bug #8187 (project relax): Status: In Progress = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #8059] RelaxFault in eliminate()

Follow-up Comment #4, bug #8059 (project relax): The solution to this problem is presented at https://mail.gna.org/public/relax-devel/2006-12/msg00031.html (Message-id: [EMAIL PROTECTED]). The bug was discussed in the thread starting at

[bug #8059] RelaxFault in eliminate()

Update of bug #8059 (project relax): Status: Need Info = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #8201] python: can't open file 'C:Program': [Errno 2] No such file or directory

Follow-up Comment #1, bug #8201 (project relax): The solution to the problem was posted by Andrew Perry (https://gna.org/users/pansapiens) in the post https://mail.gna.org/public/relax-users/2007-01/msg00010.html (Message-id: [EMAIL PROTECTED]). Barbara Dancheck confirmed the fix at

[bug #8201] python: can't open file 'C:Program': [Errno 2] No such file or directory

Update of bug #8201 (project relax): Originator Name: = Barbara Dancheck ___ Reply to this item at: http://gna.org/bugs/?8201 ___ Message sent

[task #4087] Modify the scons target 'source_dist' to create both '.tar.bz2' and '.zip' files.

Update of task #4087 (project relax): Status:None = Done Percent Complete: 0% = 100% Assigned to:None = bugman Open/Closed:

[bug #8248] Test suite failure. The model-free 'results.read()' function failed.

URL: http://gna.org/bugs/?8248 Summary: Test suite failure. The model-free 'results.read()' function failed. Project: relax Submitted by: bugman Submitted on: Friday 01/12/2007 at 01:15 Category: relax's source code

[task #3838] Splitting up and redesigning the 'pdb()' user function.

Update of task #3838 (project relax): Status: Ready For Test = Done Open/Closed:Open = Closed ___ Reply to this item at:

[bug #8682] Broken synopsis of the system/functional tests.

Update of bug #8682 (project relax): Status:None = Fixed Assigned to:None = bugman Open/Closed:Open = Closed

[bug #8996] Bugs in palmer.py

Update of bug #8996 (project relax): Status:None = Fixed Assigned to:None = bugman Open/Closed:Open = Closed Operating System:

[bug #8997] bug in palmer.py stage 2

Update of bug #8997 (project relax): Status:None = Need Info Assigned to:None = bugman ___ Follow-up Comment #1: Carl, Would it be

[bug #9093] relax is broken in Python 2.5 (failure of the RelaxError system!)

Update of bug #9093 (project relax): Status:None = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #8953] crash on mc save

Follow-up Comment #1, bug #8953 (project relax): Gary, could you attach the script to this bug report? The HTML has removed all the indentation therefore for the record this will be useful. Cheers, Edward ___ Reply to this item at:

[bug #8953] crash on mc save

Follow-up Comment #2, bug #8953 (project relax): This bug does not occur in relax versions 1.2.7 and lower. 1.2.8 and 1.2.9 may be free of the bug but I cannot test these due to the Python 2.5 failure. ___ Reply to this item at:

[bug #8953] crash on mc save

Follow-up Comment #3, bug #8953 (project relax): The bug does not occur in versions 1.2.8 or 1.2.9. I have modified the code of these version to run under Python 2.5 and the bug does not occur. Therefore it was a regression introduced between 1.2.9 and 1.2.10.

[bug #8953] crash on mc save

Update of bug #8953 (project relax): Status: Confirmed = Fixed Assigned to:None = bugman Open/Closed:Open = Closed

[bug #9101] Failure of the relax_data.read() user function with missing data.

URL: http://gna.org/bugs/?9101 Summary: Failure of the relax_data.read() user function with missing data. Project: relax Submitted by: bugman Submitted on: Tuesday 05/08/2007 at 21:43 Category: relax's source code

[bug #9101] Failure of the relax_data.read() user function with missing data.

Update of bug #9101 (project relax): Status:None = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #9238] Error in setting the heteronuclear frequency in 'maths_fns/jw_mapping.py'

Update of bug #9238 (project relax): Status:None = Fixed Assigned to:None = bugman Open/Closed:Open = Closed Operating System:

[bug #9189] Undefined functions in mf.py

Update of bug #9189 (project relax): Status:None = Fixed Assigned to:None = bugman Open/Closed:Open = Closed Operating System:

[bug #9259] Reduced spectral density mapping yielding bad values

Update of bug #9259 (project relax): Status:None = Fixed Open/Closed:Open = Closed Operating System: GNU/Linux = All systems

[bug #9388] C module compilation error on 64-bit GNU/Linux

URL: http://gna.org/bugs/?9388 Summary: C module compilation error on 64-bit GNU/Linux Project: relax Submitted by: bugman Submitted on: Sunday 06/24/2007 at 19:31 Category: relax's source code Severity:

[bug #9188] Residue selection in full_analysis.py

Update of bug #9188 (project relax): Status:None = Need Info ___ Follow-up Comment #1: Neil, if you could attach the 'local_tm/aic/results.bz2' file to this bug report it would be very

[bug #9388] C module compilation error on 64-bit GNU/Linux

Update of bug #9388 (project relax): Status:None = Invalid Assigned to:None = bugman Open/Closed:Open = Closed

[bug #9390] Failure of the manual compilation - inspect.getargspec() TypeError in Python 2.5

URL: http://gna.org/bugs/?9390 Summary: Failure of the manual compilation - inspect.getargspec() TypeError in Python 2.5 Project: relax Submitted by: bugman Submitted on: Sunday 06/24/2007 at 20:12 Category: Scons build

[bug #9390] Failure of the manual compilation - inspect.getargspec() TypeError in Python 2.5

Update of bug #9390 (project relax): Status:None = In Progress Assigned to:None = bugman ___ Follow-up Comment #1: The problem is being

[bug #9390] Failure of the manual compilation - inspect.getargspec() TypeError in Python 2.5

Update of bug #9390 (project relax): Status: In Progress = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #9732] Python 2.5

URL: http://gna.org/bugs/?9732 Summary: Python 2.5 Project: relax Submitted by: bugman Submitted on: Sunday 08/12/2007 at 11:53 Category: relax's source code Severity: 5 - Blocker

[bug #9732] Python 2.5 - failure in constructing the gradient of the global model

Update of bug #9732 (project relax): Summary: Python 2.5 = Python 2.5 - failure in constructing the gradient of the global model ___ Reply to this item at: http://gna.org/bugs/?9732

[bug #9892] CONV_LOOP error

Update of bug #9892 (project relax): Status:None = Ready For Test Assigned to:None = bugman Operating System: GNU/Linux = All systems

[bug #10022] string representation test of previous vs. current models in full_analysis

Update of bug #10022 (project relax): Status:None = Fixed Assigned to:None = bugman Open/Closed:Open = Closed Operating System:

[bug #9892] CONV_LOOP error

Update of bug #9892 (project relax): Status: Ready For Test = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #9389] AllRelaxErrors cannot be imported!

Update of bug #9389 (project relax): Status:None = Fixed Assigned to:None = bugman Open/Closed:Open = Closed

[bug #10323] jw_mapping.py: Element instance has no attribute 'num_ri'

Update of bug #10323 (project relax): Status:None = Ready For Test Assigned to:None = bugman Operating System:None = All systems

[bug #10320] bug in model-free.py; All residues must either have a local tm parameter or not

Update of bug #10320 (project relax): Status: In Progress = Ready For Test ___ Reply to this item at: http://gna.org/bugs/?10320 ___ Message sent

[bug #10320] bug in model-free.py; All residues must either have a local tm parameter or not

Update of bug #10320 (project relax): Status: Ready For Test = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #8997] bug in palmer.py stage 2

Update of bug #8997 (project relax): Status: Need Info = In Progress ___ Reply to this item at: http://gna.org/bugs/?8997 ___ Message sent

[bug #8997] bug in palmer.py stage 2

Update of bug #8997 (project relax): Status: In Progress = Fixed Open/Closed:Open = Closed Operating System: GNU/Linux = All systems

[bug #11378] relax_data.back_calc raises errors

Update of bug #11378 (project relax): Status:None = In Progress Assigned to:None = bugman ___ Follow-up Comment #1: This was first

[bug #11378] relax_data.back_calc raises errors

Update of bug #11378 (project relax): Operating System: GNU/Linux = All systems ___ Reply to this item at: http://gna.org/bugs/?11378 ___ Message sent

[bug #11383] calling relax_data.display fails

Update of bug #11383 (project relax): Status:None = Confirmed ___ Reply to this item at: http://gna.org/bugs/?11383 ___ Message sent

[bug #11004] Model elimination and Monte Carlo simultion elimination - ZeroDivisionError

Update of bug #11004 (project relax): Summary: Model elimination = Model elimination and Monte Carlo simultion elimination - ZeroDivisionError ___ Follow-up Comment #4: This bug also affects the elimination of

[bug #11004] Model elimination and Monte Carlo simultion elimination - ZeroDivisionError

Follow-up Comment #5, bug #11004 (project relax): Oh, for reference without going to the emails, the backtrace from the Monte Carlo failure is: However, I also tried the some local_tm models and got an error with model tm2 (after the command relax monte_carlo.error_analysis(run='tm2',

[bug #11004] Model elimination and Monte Carlo simultion elimination - ZeroDivisionError

Update of bug #11004 (project relax): Status: Ready For Test = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #11476] Model m0 instances break the minimise() function

Update of bug #11476 (project relax): Status: Ready For Test = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #11483] Parsing problem in ModelFree4 gets relax crash when using palmer.py

Update of bug #11483 (project relax): Status:None = Ready For Test ___ Reply to this item at: http://gna.org/bugs/?11483 ___ Message sent

[bug #11483] Parsing problem in ModelFree4 gets relax crash when using palmer.py

Update of bug #11483 (project relax): Status: Ready For Test = Fixed Open/Closed:Open = Closed ___ Reply to this item at:

[bug #11454] Constraint incorrectly supplied when using the full_analysis.py script

Follow-up Comment #4, bug #11454 (project relax): For many discussions, please see the post: https://mail.gna.org/public/relax-devel/2008-04/msg00038.html (Message-id: [EMAIL PROTECTED]) Note also that the secondary issue has been shifted and solved in bug #11476 (https://gna.org/bugs/?11476).

[bug #11799] cannot download relax

Update of bug #11799 (project relax): Status:None = Fixed Assigned to:None = bugman Open/Closed:Open = Closed Operating System:

[bug #12407] Model elimination does nothing for model-free models.

Follow-up Comment #2, bug #12407 (project relax): For the system test of the elimination of a model-free model with te = 200 ns, the error message is now: relax pipe.create(pipe_name='elim', pipe_type='mf') relax results.read(file='final_results_trunc_1.3',

[bug #12407] Model elimination does nothing for model-free models.

Follow-up Comment #4, bug #12407 (project relax): For the test_tm_51ns() system test, which checks the elimination of a model with local tm 50 ns, the last lines of print out including the traceback is now: relax model_free.select_model(model='tm4', spin_id=None) relax value.set(val=5.1e-08,

[bug #12407] Model elimination does nothing for model-free models.

Follow-up Comment #6, bug #12407 (project relax): The error is now: relax model_free.select_model(model='tm4', spin_id=None) relax value.set(val=5.1e-08, param='local_tm', spin_id=':15') relax eliminate(function=None, args=None) The local tm parameter of 5.1e-08 is greater than

  1   2   3   4   5   6   7   8   9   >