Hi to all!
I was compiling the HYPHY in the machine with FreeBSD 6.1 installed. I was executed de command sh buil.sh MP, because the hardware is a xeon dual, and show this error:
Building regex.cpp
regex.cpp:34:20: alloca.h: No such file or directory
Error during compilation

Why this error? And how can I correct this error?

Sorry de poor english
Thanks your attetion.

Dear Jackson,

Your system is probably missing a somewhat standard alloca.h header file used by gnuregx.h

Try this:

Edit strings.cpp in the Source directory. Replace #include "gnuregex.h" with #include "regex.h" on line 27. Next move the regex.cpp file out of the Source directory and recompile. Since most modern UNIX distributions already include regular expression libraries, this should try to link HyPhy against the standard library instead.

Cheers,
Sergei

Thanks Sergei.

Hi Sergei,  I have another error in the compiling the HYPHY v0.99beta,  the machine that I used was

Linux intel2 2.6.19-gentoo-r5 #1 SMP Thu Feb 22 12:12:08 BRT 2007 x86_64 Intel(R) Xeon(R) CPU            5160  @ 3.00GHz GenuineIntel GNU/Linux

And the log of compilation:


sh gtk_build.sh MP2
Linux
Checking for curl
curl_check.cpp:1:23: error: curl/curl.h: No such file or directory
Curl seems to be absent (setting up compiler options skip CURL code)
COMPILER_FLAGS= -w -c -O3 -fsigned-char -fpermissive -I/home/jackson/HYPHY_Source/GUI -I/home/jackson/HYPHY_Source/Source -I/home/jackson/HYPHY_Source/Source/SQLite -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include   -D__HYPHY_NO_CURL__
+-----------------------------------------------------------+
|Building a multi-threaded HYPHYKernelMP with setconcurrency|
+-----------------------------------------------------------+
File HYNetInterface.cpp is up to date
File Net.cpp is up to date
File baseobj.cpp is up to date
File batchlan.cpp is up to date
File batchlan2.cpp is up to date
File calcnode.cpp is up to date
File category.cpp is up to date
File error.cpp is up to date
File fisher_exact.cpp is up to date
File likefunc.cpp is up to date
File list.cpp is up to date
File matrix.cpp is up to date
File nexus.cpp is up to date
File parser.cpp is up to date
File parser2.cpp is up to date
File polynoml.cpp is up to date
File regex.cpp is up to date
File scfg.cpp is up to date
File sequence.cpp is up to date
File site.cpp is up to date
File strings.cpp is up to date
File main-GTK.cxx is up to date
File mainGTK.cxx is up to date
SQLite File attach.c is up to date
SQLite File auth.c is up to date
SQLite File btree.c is up to date
SQLite File btree_rb.c is up to date
SQLite File build.c is up to date
SQLite File copy.c is up to date
SQLite File delete.c is up to date
SQLite File expr.c is up to date
SQLite File func.c is up to date
SQLite File hash.c is up to date
SQLite File insert.c is up to date
SQLite File main.c is up to date
SQLite File opcodes.c is up to date
SQLite File os.c is up to date
SQLite File pager.c is up to date
SQLite File parse.c is up to date
SQLite File pragma.c is up to date
SQLite File printf.c is up to date
SQLite File random.c is up to date
SQLite File select.c is up to date
SQLite File table.c is up to date
SQLite File tokenize.c is up to date
SQLite File trigger.c is up to date
SQLite File update.c is up to date
SQLite File util.c is up to date
SQLite File vacuum.c is up to date
SQLite File vdbe.c is up to date
SQLite File where.c is up to date
File HYBaseGUI.cpp is up to date
File HYButton.cpp is up to date
File HYButtonBar.cpp is up to date
File HYChartWindow.cpp is up to date
File HYCheckBox.cpp is up to date
File HYComponent.cpp is up to date
File HYConsoleWindow.cpp is up to date
File HYDBWindow.cpp is up to date
File HYDataPanel.cpp is up to date
File HYDialogDefs.cpp is up to date
File HYEventTypes.cpp is up to date
File HYGraphicPane.cpp is up to date
File HYLabel.cpp is up to date
File HYModelWindow.cpp is up to date
File HYObjectInspector.cpp is up to date
File HYParameterTable.cpp is up to date
File HYPlatformBootsrapWindow.cpp is up to date
File HYPlatformButton.cpp is up to date
File HYPlatformButtonBar.cpp is up to date
File HYPlatformChartWindow.cpp is up to date
File HYPlatformCheckBox.cpp is up to date
File HYPlatformComponent.cpp is up to date
File HYPlatformConsoleWindow.cpp is up to date
File HYPlatformDBWindow.cpp is up to date
File HYPlatformDataPanel.cpp is up to date
File HYPlatformGWindow.cpp is up to date
File HYPlatformGraphicPane.cpp is up to date
File HYPlatformLabel.cpp is up to date
File HYPlatformModelWindow.cpp is up to date
File HYPlatformPWindow.cpp is up to date
File HYPlatformParameterTable.cpp is up to date
File HYPlatformPullDown.cpp is up to date
File HYPlatformSequencePane.cpp is up to date
File HYPlatformTWindow.cpp is up to date
File HYPlatformTable.cpp is up to date
File HYPlatformTextBox.cpp is up to date
File HYPlatformTreePanel.cpp is up to date
File HYPlatformUtils.cpp is up to date
File HYPlatformWindow.cpp is up to date
File HYPullDown.cpp is up to date
File HYSequencePanel.cpp is up to date
File HYTable.cpp is up to date
File HYTextBox.cpp is up to date
Building HYTreePanel.cpp
HYTreePanel.cpp: In member function 'void _HYTreePanel::HandleTreeSave(long int, _String)':
HYTreePanel.cpp:6524: error:   crosses initialization of '_TheTree* me'
Error during compilation
jackson@intel2 ~/HYPHY_Source $ gcc -v
Using built-in specs.
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-4.1.1-r3/work/gcc-4.1.1/configure --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.1.1 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.1/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.1/include/g++-v4 --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --disable-altivec --enable-nls --without-included-gettext --with-system-zlib --disable-checking --disable-werror --enable-secureplt --disable-libunwind-exceptions --enable-multilib --disable-libmudflap --disable-libssp --disable-libgcj --enable-languages=c,c++,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu
Thread model: posix
gcc version 4.1.1 (Gentoo 4.1.1-r3)


I compiled the same version in the one machine with FreeBSD6.1 and don't have anyone error.

How can I correct this error?

Sorry the english.
Thanks your attention.
Congratulations for HYPHY's Developers

Dear Jackson,

This is gcc.4.1 being picky. I'll modify the syntax in the file it complained about to conform with the variable scoping conventions.

Thanks for reporting this issue,
Sergei

Dear Sergei,

The alteration in source is below:



void    _HYTreePanel::HandleTreeSave (long c, _String filePath)
{
       FILE*           theFile = doFileOpen (filePath.sData,"w");
       _TheTree        * me; //    = LocateMyTreeVariable();
       if (theFile)
       {
               switch (c)
               {
                       case 1:
                               {
                                       _String res = GetTreeString();
                                       fprintf (theFile,"#NEXUS\nBEGIN TREES;\n\tTree %s = %s;\nEND;",GetTitle().Cut(5,-1).getStr(),res.getStr());
                               }
                               break;
                       case 2:
                       case 3:
                               me    = LocateMyTreeVariable();
                               if (me)
                               {
                                       if (c==2)
                                       {
                                               _List           nodeNames;
                                               _AVLListXL  nodeRemap (&nodeNames);
                                               _CalcNode*  cNode  = me->LeafWiseTraversal(true);
                                               long            nodeCounter = 1;
                                               fprintf (theFile,"#NEXUS\nBEGIN TREES;\n\tTRANSLATE");

I would like to know as to install the HYPHY being twirled in MPI?
Perhaps I'll buy 3 Intel Xeon 2 DualCore, in the total of 12 CPUs, and if it obtained to make to twirl the HYPHY distributing and speeding up the analyses in the 12 CPUs very went to be good.
The server who reported the error of the compilation is a Intel Xeon 2 DualCore, when compels in MP2, the HYPHY distributes the analyses in the 4 CPUs?
Sorry de poor english
Thanks your attetion.