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