Hi Sergei,

A few questions -

Firstly:
I've just upgraded my machine to run Leopard/Mac OS X 10.5, and I'm having some problems with HyPhy on the upgraded system (the machine is a 2x2.66 GHz Intel).

Firstly, the text that gets written to the log/console window tends to bunch up together on the left side, squeezing all the characters into the place taken usually by 10 characters (see image below). I've tried changing the setting for the console fonts, but it happens under each typeface and size I tried.

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I wondered if you've heard of this problem elsewhere and maybe have suggestions how to deal with this?

Secondly:
Even if this problem persists, it'd be fine if I could somehow pipe the text that appears in the console to a file I could read elsewhere, using a text editor. I've hunted around for a command or menu or something that will do this, but couldn't find out how to make this happen. Would be great if you could let me know if/how that's possible.

Thirdly:
I also had a go compiling the source code on this machine - despite being almost completely clueless about how such things work.

It doesn't compile - even though /usr/lib seems to contain the required libcurl, libssl, and libcrypto.

When I run build.sh, I get the following output - any suggestions (even very basic ones - I really have no clue what this stuff means, where even to begin trying to fix this) on how to deal with this much appreciated.

Best wishes

Aidan
Code:

mac-gibson18:HYPHY_Source budd$ bash build.sh SP
Darwin
Checking for curl
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libssl.dylib load command 8 unknown cmd field
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libcrypto.dylib load command 8 unknown cmd field
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libcurl.dylib load command 8 unknown cmd field
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/libstdc++.dylib load command 8 unknown cmd field
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libSystem.dylib unknown flags (type) of section 6 (__TEXT,__literal16) in load command 0
/usr/bin/ld: /usr/lib/libSystem.B.dylib unknown flags (type) of section 6 (__TEXT,__literal16) in load command 0
collect2: ld returned 1 exit status
Curl seems to be absent (setting up compiler options skip CURL code)
+--------------------------------------+
|Building a single threaded HYPHYKernel|
+--------------------------------------+
COMPILER=g++, gcc
COMPILER_FLAGS= -D __UNIX__ -w -c -fsigned-char -fast -fpermissive -I/Users/budd/Desktop/hyphy_source/HYPHY_Source/Source -I/Users/budd/Desktop/hyphy_source/HYPHY_Source/Source/SQLite -D INTPTR_TYPE=long  -D__HYPHY_NO_CURL__
Building HYNetInterface.cpp
Complete
Building Net.cpp
Complete
Building baseobj.cpp
....
....
Building SQLite file vdbe.c
Complete
Building SQLite file where.c
Complete
Linking HYPHY
g++ -w -fsigned-char -D__HYPHY_NO_CURL__ -o HYPHY obj_SP/HYNetInterface.cpp.o obj_SP/Net.cpp.o obj_SP/attach.c.o obj_SP/auth.c.o obj_SP/baseobj.cpp.o obj_SP/batchlan.cpp.o obj_SP/batchlan2.cpp.o obj_SP/bgm.cpp.o obj_SP/btree.c.o obj_SP/btree_rb.c.o obj_SP/build.c.o obj_SP/calcnode.cpp.o obj_SP/category.cpp.o obj_SP/copy.c.o obj_SP/delete.c.o obj_SP/error.cpp.o obj_SP/expr.c.o obj_SP/fisher_exact.cpp.o obj_SP/func.c.o obj_SP/hash.c.o obj_SP/hyphyunixutils.cpp.o obj_SP/insert.c.o obj_SP/likefunc.cpp.o obj_SP/list.cpp.o obj_SP/main-unix.cxx.o obj_SP/main.c.o obj_SP/matrix.cpp.o obj_SP/nexus.cpp.o obj_SP/opcodes.c.o obj_SP/os.c.o obj_SP/pager.c.o obj_SP/parse.c.o obj_SP/parser.cpp.o obj_SP/parser2.cpp.o obj_SP/polynoml.cpp.o obj_SP/pragma.c.o obj_SP/printf.c.o obj_SP/random.c.o obj_SP/regex.cpp.o obj_SP/scfg.cpp.o obj_SP/select.c.o obj_SP/sequence.cpp.o obj_SP/site.cpp.o obj_SP/strings.cpp.o obj_SP/table.c.o obj_SP/tokenize.c.o obj_SP/trigger.c.o obj_SP/update.c.o obj_SP/util.c.o obj_SP/vacuum.c.o obj_SP/vdbe.c.o obj_SP/where.c.o -lm
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libm.dylib unknown flags (type) of section 6 (__TEXT,__literal16) in load command 0
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/libstdc++.dylib load command 8 unknown cmd field
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libSystem.dylib unknown flags (type) of section 6 (__TEXT,__literal16) in load command 0
/usr/bin/ld: /usr/lib/libSystem.B.dylib unknown flags (type) of section 6 (__TEXT,__literal16) in load command 0
collect2: ld returned 1 exit status
Finished
 

Dear Aidan,

Sorry, I missed your original post somehow!

The text blurring bug appeared in OS X.4; it has something to do with stock tools used to render text using OS widgets. As you discovered on your own, you can fix the issue by resizing the console. I'll check the text function programming reference again and see if there is anything I can do to rectify the problem.

As far as compile time errors go, he ones you report are new to me. I haven't seen these linker messages before. Can you compile trivial programs like:

Code:

#include <stdout.h>

int main(int argc, char *argv[])
{
     printf ("Hello world\n");
     return 0;
}

 

? It looks like you may have a system wide linker issue, but let's check on a trivial program first.

Cheers,
Sergei

Dear Aidan,

Glad that it worked.
I am still not sure what is causing the blurred text in the console. I checked the most recent Apple Developer API for text rendering and could find nothing relevant. I'll see if I can force text layout updates when new text is printed to the console.

Cheers,
Sergei