Hi Hiram, I don't know if this makes a difference, but I've just been building the isPcrSrc folder and its sub-directories.
I do not get any errors building the lib dir, thanks to your fix on the warnings. There is a jkweb.a built, but it's in lib/i386. That is not my machine type: $ echo $MACHTYPE i686-pc-cygwin I deleted the isPcr directory, and re-downloaded it. I think the problem IS that I'm just building that. It comes with the i386 jkweb.a, but doesn't come with either the source, or an i686 version. So I guess I need to download the whole tree, build jkweb.a, then go the isPcrSrc and build there. Should that work? 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
