Hi Hiram,
So make libs gives errors
for cd lib && make
/usr/bin/ranlib: file: x86_64/jkweb.a(gifwrite.o) has no symbols
/usr/bin/ranlib: file: x86_64/jkweb.a(vGif.o) has no symbols
for cd jkownlib && make
/usr/bin/ranlib: file: ../../lib/x86_64/jkhgap.a(knetUdc.o) has no symbols
Then for cd hg followed by make compile ends with the following errors
Undefined symbols:
"_png_write_png", referenced from:
_mgSaveToPng in jkweb.a(pngwrite.o)
"_png_create_write_struct", referenced from:
_mgSaveToPng in jkweb.a(pngwrite.o)
"_png_set_IHDR", referenced from:
_mgSaveToPng in jkweb.a(pngwrite.o)
"_png_destroy_write_struct", referenced from:
_mgSaveToPng in jkweb.a(pngwrite.o)
_mgSaveToPng in jkweb.a(pngwrite.o)
_mgSaveToPng in jkweb.a(pngwrite.o)
"_png_create_info_struct", referenced from:
_mgSaveToPng in jkweb.a(pngwrite.o)
"_png_init_io", referenced from:
_mgSaveToPng in jkweb.a(pngwrite.o)
"_png_set_rows", referenced from:
_mgSaveToPng in jkweb.a(pngwrite.o)
"_png_set_longjmp_fn", referenced from:
_mgSaveToPng in jkweb.a(pngwrite.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [compile] Error 1
make: *** [hgGene.compile] Error 2
I set $PNGINCL to /usr/local/include/libpng14. I tried different directories
with the png.h file in them and tried reinstalling libpng without luck. I also
tried make clean and then manually make in lib and jkownlib with similar
results.
Also, all of your instructions refer to the directory as kent/src but my file
simply unzipped to $HOME/jksrc and everything that would be in the src
directory is in there. Is that a problem?
- Jacob
On Oct 27, 2010, at 11:38 AM, Hiram Clawson wrote:
> Good Morning Jacob:
>
> Something has gone haywire. With your USE_ variables defined and in your
> shell
> environment properly. Go to the top of your source tree and run:
> $ cd src
> $ make clean
> $ make libs
> $ cd hg
> $ make compile
> $ make install DESTDIR=... CGI_BIN=...
>
> Please note the instructions on this in the source tree file:
> src/product/README.building.source
> Check the "Known problems:" listing near the end of this document
> for anything you many encounter. If you come up with a new problem
> let me know and we can get it documented. Max's instructions are interesting,
> but they are specific for his location.
>
> --Hiram
>
> Jacob C Schwartz wrote:
>>> From: jacob schwartz <[email protected]>
>>> Date: October 27, 2010 10:08:41 AM MDT
>>> To: Mary Goldman <[email protected]>, Galt Barber <[email protected]>,
>>> Maximilian Haussler <[email protected]>
>>> Subject: Re: [Genome] install Mac OS X 10.6.4
>>>
>>>
>>> Hi Mary, I installed Libpng14 and samtools and zlib and tried setting the
>>> USE variables. So I've created a new problem.
>>> 1) It will either return error about jkweb.a(pngwrite.o) has no symbols if
>>> I add the -lssl and -lcrypto to the MYSQLLIBS like you recommended and do
>>> make without setting USE variables, the PNGINCL variable or the SAMDIR
>>> variable.
>>> 2) If I set USE variables to 1 is get an error jkweb.a(gifwrite.o) has no
>>> symbols.
>>> 3) If I try messing with the PNGINCL variable I get an terrible error about
>>> invalid option "-Wno-double-somethingorother" when the make is just a few
>>> lines in.
>>> I suppose I need another GIF library? Do you know where I look for that?
>>>
>>> Also, Max, the protocol you've recommended is the one that has worked best
>>> for me so far. I'm close, I think I'm just missing some critical component.
>>>
>>> Thanks so much for your help,
>>>
>>> Jacob
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