

 Recognised errors and problems with Simfit: 
 ===========================================

 Details for Simfit: version 6

 http://www.simfit.manchester.ac.uk


 The following problems have been recognised. 

 1) Problem 1: corrupted configuration files
 2) Problem 2: NAG Library Mark 20 DLLs
 3) Problem 3: protected program files trees 
 4) Problem 4: ghostscript and start_process_and_wait@ in Linux
 5) problem 5: incorrect p-values for negative r_values


 1) Problem 1
 ============

 Summary
 -------
 This problem can be caused by impatient double clicking or
 crashing out of simfit leaving corrupted files, or by giving
 some simfit configuration files the read_only attribute.

 Description
 -----------
 Simfit does not use the registry for configuration, it
 uses copies of ASCII text *.cfg configuration files,
 e.g., w_simfit.cfg. Also temporary files with names like
 f$??????.tmp are created, and in addition, the NAG library
 version writes to the file nagifail.txt.

 If any of these files are corrupted, e.g. by impatient mouse
 clicking during write operations, or in some cases where
 write/read access is prevented, then Simfit will crash with
 error messages such as

 ...Data error (cyclic redundancy check)

 when it attempts write/read. The solution is to run the
 Windows utility CHKDSK, or similar, to repair or delete all
 corrupted files. Simfit will simply re-write default versions
 of the configuration files. Also, to limit the possibility of
 such errors, users should routinely use the configuration
 option to delete all f$??????.tmp files at close down, and so
 prevent build up, which progressively slows down many Simfit
 write/read operations, as Simfit frequently scans the list of
 all local f$??????.tmp files before assigning new temporary
 file names.

 2) Problem 2
 ============

 Summary
 -------
 This problem only occurs running the NAG library Mark 20 version
 of simfit on machines that have chips more recent than P4.

 Description
 -----------
 The NAG library Mark 20 DLLs may automatically link to MKL_P4.DLL
 in the NAG library folder. This DLL is configured to get the best 
 out of the P4 chip, but using it will lead to problems with more
 recent chips. For instance, access violations are known to happen
 with the P5 and AMD64 chips. If your NAG library version of Simfit
 is Mark 20 and it exhibits such behaviour, the solution is to
 delete MKL_P4.DLL, or rename the file MKL_P4.DLL to something like
 MKL_P4.BAK. This will simply force the NAG library DLLs to use
 default machine operations instead of the ones optimised for P4
 which are causing the problem. 

 3) Problem 3 (Only refers to Simfit versions prior to 6.2.6)
 ============

 Summary
 -------
 This problem only occurs with operating systems from Vista onwards
 where the C:\Program Files\tree is protected, and users are provided
 with a virtual tree. The problem has been resolved for versions
 of Simfit from 6.2.6 onwards, as Simfit will not attempt to write
 to any local files.

 Description (Only applies to versions of Simfit before 6.2.6)
 ----------- 
 With operating systems before Vista, all configuration files are
 read from and written to the Simfit folder, and are therefore all
 accessed as local files. If Simfit is installed in a protected
 tree and only used by normal users then all will be well, as the
 configuration files will be in the users virtual tree. However,
 if an admistrator runs w_simfit.exe with adminstrator privileges,
 the configuration files will be in the Simfit folder. This will
 then prevent any future non-privileged users from re-configuring
 Simfit, because Simfit will read the configuration files created
 by the adminstrator. There are two solutions for Simfit versions
 before 6.2.6.

 a) Do not install Simfit in a protected tree
 b) Simply delete all .cfg files from the true Simfit folder and
    allow Simfit to create defaults in the user's virtual tree.   
 
 4) Problem 4
 ============  

 Summary
 -------
 Simfit executes binaries using the function call

 k = start_process_and_wait@(program, command, time)

 which works most of the time provided that the advanced options to
 change the waiting times are used, and file names with spaces are quoted.
 This should return k = 0 on satisfactory exit, but this does not always
 happen in Wine/Linux, and so the advanced option to suppress Windows
 error messges should always be used.  
 
 Description
 -----------
 When Simfit attempts to run the built-in Linux version of ghostscript
 there is a problem that cannot be cured by altering the wait time and
 quoting file names with spaces. The processes spawned by ghostscript
 to create graphics files from *.eps files for example are not always
 finished when start_process_and_wait@ exits (with k = -1) and the graphics
 files remain unfinished. An additional step to prevent this happening has
 been added to Simfit at 6.2.2, which now issues a warning to indicate that
 further editing of wait time may possibly be needed if the graphics
 file creation has not terminated properly. This warning can be ignored if
 graphics files have been satisfactorily created. Alternatively, like the
 other auxiliaries, the Windows version of ghostscript may be installed
 in the Wine environment. 

  5) Problem 5 
  ============

  At 7.2.1 an error was introduced into Pearson correlation analysis in
  that the lower triangle of p-values was in error when the corresponding
  r-value was negative.

  To summarise: r(i,j) > 0 --> p(i,j) correct
                r(i,j) < 0 --> p(i,j) incorrect

  This mistake was repaired at 7.2.5  
 



