[Genome] How to Build isPcr

[Gregory Dougherty]

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" <hi...@soe.ucsc.edu>
To: "Gregory Dougherty" <gr...@soe.ucsc.edu>
Cc: "genome" <gen...@lists.soe.ucsc.edu>
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" <gr...@soe.ucsc.edu>
To: "Hiram Clawson" <hi...@soe.ucsc.edu>
Cc: "genome" <gen...@lists.soe.ucsc.edu>
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" <hi...@soe.ucsc.edu>
To: "genome" <gen...@lists.soe.ucsc.edu>
Cc: "Gregory Dougherty" <gr...@soe.ucsc.edu>
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

[Vanessa Kirkup Swing]

Dear Greg,

Thank you for your helpful suggestions. Unfortunately, the READMEs that
you are looking at aren't READMEs that are generated by UCSC, but by
Kent Informatics, Inc., but I will forward your suggestions.

Vanessa Kirkup Swing
UCSC Genome Bioinformatics Group

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