Dear Konrad,

libcurl (and libssl) are not essential for HyPhy - they simply enable the GetURL command, which is not used for most analyses. Setting the D__HYPHY_NO_CURL__ will toggle code #ifdefs to exclude curl specific code, but my trivial build script will still try to link the libraries. Scan the build.sh (or gtk_build.sh) file for LINKER_FLAGS and remove references to lcurl, lssl and lcrypto.

On the other hand, curl is a handly thing to have; it compiles out of the box (including SuSE systems) and can be downloaded from Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

HTH,
Sergei

Dear Konrad,

Quote:


Either that, or pkg-config is not in the standard $PATH. If you have any form of GTK (e.g. Gnome) installed on SuSE, then there should be pkg-config somewhere in your system; you may have to fun a 'find' command to see if it's present.

Cheers,
Sergei

Dear Konrad,

[quote author=konrad  link=1128608247/0#4 date=1128963279]Found the problem: I was missing GTK2-devel and some other -devel packages. Everything now builds properly (with CURL), but on running HYPHY_GTK it complains that it cannot find "a required GTKResources directory" and suggests "Please use BASEPATH= command line option...", even though GTKResources is sitting right there in the installation directory I am running from.
[/quote]

HyPhy uses the getcwd command to identify where it is being launched from. Unless you have cd'ed to the build directory and launched HYPHY_GTK from the command line (which should work), it may not point to the right place. Try running
[code]
$HYPHY_GTK BASEPATH=/absolute path to hyphy with trailing slash
[/code]

and see if that helps.
Cheers,
Sergei

Dear Konrad,

[quote author=konrad  link=1128608247/0#6 date=1129116952]

This is what I did. The path quoted back to me in the error message is the correct path. Specifying BASEPATH makes no difference (unsurprising, since it's already correct).

[/quote]

This is very odd indeed. HyPhy will report this message if can't find the directory, or if the directory contains no (or only hidden) files. If you do 'ls GTKResources', are you able to see a number of png and xpm files (with numeric names)?

Cheers,
Sergei

Hmm, I am at a loss as to what could be causing this problem, since HyPhy uses standard 'dirent.h' based file system calls to generate a list of files inside a directory.

Does the path to HYPHY source include any nonstandard characters (e.g. spaces etc), or the '~' shorthand for the home directory (which I don't believe is understood by dirent functions)? When the error dialog is displayed, does HyPhy report a complete absolute path to GTKResources?

I have not come across this behavior before; may take a few tries to get this sorted out.

Cheers,
Sergei

Dear Konrad,

[quote author=konrad  link=1128608247/0#10 date=1129132543]No nonstandard characters, and yes it reports the full path (no ~).
[/quote]

Would you mind pasting this in place of the same function in HYPlatformUtils.cpp in the GUI directory, recompiling the GTK version, running it from the console and telling me what the code printed (if anything)?

[code]
#define KONRAD_DEBUG

//__________________________________________________________________________________
char      ScanDirectoryForFileNames (_String& source, _List& rec, bool recurse)
{
     DIR * dirPntr = opendir (source.sData);
     if (dirPntr)
     /* source directory exists */
     {
           struct dirent * curEntry = nil;
                 
           while (curEntry = readdir (dirPntr))
           // index thru the items
           {
                 _String childDir (curEntry->d_name);
                 if (childDir[0] != '.') // invisible file
                 {
                       #ifdef KONRAD_DEBUG
                             printf ("ScanDirectoryForFileNames::checking item %s with d_type of %x\n", childDir.sData, curEntry->d_type);
                       #endif
                       childDir = source & '/' & childDir;                  
                       if (curEntry->d_type == DT_DIR)
                       // a directory
                       {
                             if (recurse)
                                   ScanDirectoryForFileNames (childDir,rec,true);
                       }
                       else
                             if (curEntry->d_type == DT_REG)
                                   rec && & childDir;
                 }
           }
           closedir (dirPntr);
     }
     #ifdef KONRAD_DEBUG
     else
           printf ("ScanDirectoryForFileNames::Failed to open %s with opendir\n", source.sData);
     #endif
     return '/';
}
[/code]

I added some more printf statements to this function to see what was happening, and bizarrely this caused the program behaviour to change. It now continues running ScanDirectoryForFileNames for the directories UserAddins, TreeAddIns, GeneticCodes and SubstitutionModels (all items have d_type = 0). It then opens the HYPHY Console with text "Loaded 12 genetic code tables from /home/konrad/HyPhy/HYPHY_Source/GeneticCodes" and pops up a warning "The following error occurred: Bad symbols in expression". In my xterm it prints:
** (HYPHY_GTK:7785): WARNING **: Invalid UTF8 string passed to pango_layout_set_text()
This warning occurs 3 times when I keep clicking "Skip further messages".
It then prints: "I couldn't find any valid model templates in '/home/konrad/HyPhy/HYPHY_Source/SubstitutionModels'. Please check your installation of HYPHY for missing files.
Please cite S.L. Kosakovsky Pond, S. D. W. Frost and S.V. Muse. (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679 if you use HyPhy in a publication" in the HYPHY Console.
After this I am able to operate the menus in the HYPHY Console.
On attempting to open the p51.nex example file, the console disappears and the output to the xterm is:
** (HYPHY_GTK:7785): WARNING **: Invalid borders specified for theme pixmap:
       /home/konrad/HyPhy/HYPHY_Source/GTKResources/theme/entry1.png,
borders don't fit within the image

(HYPHY_GTK:7785): Gdk-CRITICAL **: file gdkdraw.c: line 265 (gdk_drawable_set_colormap): assertion `cmap == NULL || gdk_drawable_get_depth (drawable) == cmap->visual->depth' failed

(HYPHY_GTK:7785): Gdk-CRITICAL **: file gdkdraw.c: line 265 (gdk_drawable_set_colormap): assertion `cmap == NULL || gdk_drawable_get_depth (drawable) == cmap->visual->depth' failed

(HYPHY_GTK:7785): Gdk-CRITICAL **: file gdkdraw.c: line 265 (gdk_drawable_set_colormap): assertion `cmap == NULL || gdk_drawable_get_depth (drawable) == cmap->visual->depth' failed

(HYPHY_GTK:7785): Gdk-CRITICAL **: file gdkdraw.c: line 265 (gdk_drawable_set_colormap): assertion `cmap == NULL || gdk_drawable_get_depth (drawable) == cmap->visual->depth' failed

(HYPHY_GTK:7785): Gdk-CRITICAL **: file gdkdraw.c: line 265 (gdk_drawable_set_colormap): assertion `cmap == NULL || gdk_drawable_get_depth (drawable) == cmap->visual->depth' failed

(HYPHY_GTK:7785): Gdk-WARNING **: Using Xft rendering requires the drawable argument to
have a specified colormap. All windows have a colormap,
however, pixmaps only have colormap by default if they
were created with a non-NULL window argument. Otherwise
a colormap must be set on them with gdk_drawable_set_colormap
Segmentation fault

Here is the final part of the function containing all statements I added (the "not a directory item" statement is output every time, the others never):
[code]

     if (curEntry->d_type == DT_DIR)
     // a directory
     {
#ifdef KONRAD_DEBUG
     printf ("ScanDirectoryForFileNames::%s detected as directory item.\n", childDir.sData);
#endif
     if (recurse)
#ifdef KONRAD_DEBUG
     printf ("Recursing.\n");
#endif
      ScanDirectoryForFileNames (childDir,rec,true);
     }
     else
#ifdef KONRAD_DEBUG
     printf ("ScanDirectoryForFileNames::%s not a directory item.\n", childDir.sData);
#endif
     if (curEntry->d_type == DT_REG)
#ifdef KONRAD_DEBUG
       printf ("ScanDirectoryForFileNames::%s detected as DT_REG item.\n", childDir.sData);
#endif
      rec && & childDir;
    }
   }
   closedir (dirPntr);
  }
  #ifdef KONRAD_DEBUG
  else
   printf ("ScanDirectoryForFileNames::Failed to open %s with opendir\n", source.sData);
  #endif
  return '/';
}

[/code]