Well, I got it to build. things I discovered along the way:
1: The README in isPcrSrc needs to be updated. Specifically, it says:
1. Create the environment variable MACHTYPE. To do this first type
echo $MACHTYPE
from the command line to see if this environment variable
exists. If it doesn't please create it like so:
export MACHTYPE=unixLike
if you are using the bash shell, or
setenv MACHTYPE unixLike
under the tcsh or csh.
What it NEEDS to say is:
1. Check that the environment variable MACHTYPE
exists on your system. It should exist on Unix/Linux.
(And making this on non-Unix systems is beyond
the scope of this README). The default MACHTYPE is often a
long string: "i386-redhat-linux-gnu"
which will not function correctly in this build environment.
It needs to be something simple such as one of:
i386 i686 sparc alpha x86_64 ppc etc ...
with no other alpha characters such as: -
To determine what your system reports itself as, try the
uname options: 'uname -m' or 'uname -p' or 'uname -a'
on your command line. If necessary set this environment variable.
Do this under the bash shell as so:
MACHTYPE=something
export MACHTYPE
or under tcsh as so:
setenv MACHTYPE something
and place this setting in your home directory .bashrc or .tcshrc
environment files so it will be set properly the next time you
login. Remember to "export" it as show here for the bash shell.
I'm guessing that part of what hurt me was my machine type being
i686-cygwin..., rather than just i686. (Yep, I just rebuilt with MACHTYPE set
to i686, and it all built).
2: When I I had to build lib, AND build jkOwnLib. 3a. ALTERNATE PATH: mentions
the first, but not the second.
3: The people on this list are very helpful, especially Hiram.
Thank you
Greg
----- Original Message -----
From: "Hiram Clawson" <[email protected]>
To: "Gregory Dougherty" <[email protected]>
Cc: "genome" <[email protected]>
Sent: Friday, July 23, 2010 9:00:02 AM GMT -06:00 US/Canada Central
Subject: Re: Finding where Primers hit
Go back to your 'make libs' step and see what error you have there.
Check these instructions in the source tree:
http://genome-test.cse.ucsc.edu/~kent/src/unzipped/product/README.building.source
--Hiram
----- Original Message -----
From: "Gregory Dougherty" <[email protected]>
To: "Hiram Clawson" <[email protected]>
Cc: "genome" <[email protected]>
Sent: Friday, July 23, 2010 6:44:03 AM GMT -08:00 US/Canada Pacific
Subject: Re: Finding where Primers hit
Hi Hiram,
Thank you, that gets me a lot closer. Unfortunately, now I get an error trying
to build jkweb.a:
gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_
-Wformat -Wimplicit -Wuninitialized -Wreturn-type -I../inc -I..
/../inc -I../../../inc -I../../../../inc -c gfPcr.c
make[2]: *** No rule to make target `../../lib//jkweb.a', needed by `gfPcr'.
Stop.
make[2]: Leaving directory `isPcr33/isPcrSrc/isPcr/gfPcr'
Thank you for your help.
Greg
----- Original Message -----
From: "Hiram Clawson" <[email protected]>
To: "genome" <[email protected]>
Cc: "Gregory Dougherty" <[email protected]>
Sent: Thursday, July 22, 2010 11:19:37 PM GMT -06:00 US/Canada Central
Subject: Re: Finding where Primers hit
Good Evening Greg:
After working with cygwin a bit here this evening, I have this update to enable
you to build
the kent source tree:
http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables#cygwin_compile_issues
I'm still working on trying to get MySQL functioning ...
--Hiram
I'll check this in my CygWin environment later today to see what the error is.
A simple cast of some type should eliminate this particular error. It has been
some
time since I've tried the compile under CygWin, I don't know if there may be
other
errors lurking. They should be manageable.
--Hiram
Gregory Dougherty wrote:
> I love when my situation changes on the fly.
>
> I'm now getting a dedicated (virtual) server. Were hoping to run isPcr or
> gfPcr AND Tomcat (serving up a Google Web Toolkit application) on a 2 CPU, 4
> GB RAM server. xxPcr will only be serving up the human genome. This is
> expected to work, yes?
>
> I'm trying to build the isPcr source tree using Cygwin. aliType.c builds
> correctly, but apacheLog.c fails. cc1 informs me that it is treating
> warnings as errors, and that at lines 92 and 119 , in function
> apacheAccessLogParse "error: array subscript as type 'char'".
>
> I have gcc 4.3.4.
>
> Should I be able to build this under Cygwin? Am I doing something stupid? I
> believe I completely followed the instruction in the isPcrSrc README.
>
> TIA,
>
> Greg
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