From bryanlepore at mail.utexas.edu Tue Jan 17 19:46:06 2006 From: bryanlepore at mail.utexas.edu (Bryan W. Lepore) Date: Tue Jan 17 19:46:11 2006 Subject: [Discuss] values.h for stamp mac os x compile Message-ID: please pardon the naive question: i'm trying to use gcc on mac os x to compile stamp_43, which needs values.h in murzin_P.c: gcc -c -g -I. murzin_P.c murzin_P.c:38:20: values.h: No such file or directory this should be with the compiler, right? or, what provides values.h? (no obvious google answers). -bryan From jon at compbio.dundee.ac.uk Wed Jan 18 00:02:58 2006 From: jon at compbio.dundee.ac.uk (Jonathan Barber) Date: Wed Jan 18 00:03:05 2006 Subject: [Discuss] values.h for stamp mac os x compile In-Reply-To: References: Message-ID: <20060118000258.GA31135@flea.compbio.dundee.ac.uk> On Tue, Jan 17, 2006 at 01:46:06PM -0600, Bryan W. Lepore wrote: > please pardon the naive question: i'm trying to use gcc on mac os x to compile > stamp_43, which needs values.h in murzin_P.c: > > gcc -c -g -I. murzin_P.c > murzin_P.c:38:20: values.h: No such file or directory > > this should be with the compiler, right? or, what provides values.h? (no > obvious google answers). Off the top of my head (I don't have the stamp code in front of me), the file murzin_P.c is refering to is /usr/include/values.h from the standard C library. According to my of this header (glibc 2.3.3), it's been replaced by either limits.h or float.h. I don't have the stamp source code to hand, but suspect that either the include statement is incorrect: #include "values.h" /* instead of */ #include or you don't have a values.h and you instead need: #include #include Hope this helps. > -bryan -- Jonathan Barber High Performance Computing Analysis Tel. +44 (0) 1382 86389 From geoff at compbio.dundee.ac.uk Wed Jan 18 11:03:25 2006 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Wed Jan 18 11:03:40 2006 Subject: [Discuss] values.h for stamp mac os x compile In-Reply-To: <20060118000258.GA31135@flea.compbio.dundee.ac.uk> References: <20060118000258.GA31135@flea.compbio.dundee.ac.uk> Message-ID: Tom, Could you take a look at this? STAMP 4.3 used to compile fine on OSX, so there must be a fairly recent change. Many thanks, Geoff. On Wed, 18 Jan 2006, Jonathan Barber wrote: > On Tue, Jan 17, 2006 at 01:46:06PM -0600, Bryan W. Lepore wrote: >> please pardon the naive question: i'm trying to use gcc on mac os x to compile >> stamp_43, which needs values.h in murzin_P.c: >> >> gcc -c -g -I. murzin_P.c >> murzin_P.c:38:20: values.h: No such file or directory >> >> this should be with the compiler, right? or, what provides values.h? (no >> obvious google answers). > > Off the top of my head (I don't have the stamp code in front of me), > the file murzin_P.c is refering to is /usr/include/values.h from the > standard C library. According to my of this header (glibc 2.3.3), it's > been replaced by either limits.h or float.h. > > I don't have the stamp source code to hand, but suspect that either the > include statement is incorrect: > > #include "values.h" > /* instead of */ > #include > > or you don't have a values.h and you instead need: > #include > #include > > Hope this helps. > >> -bryan > -- > Jonathan Barber > High Performance Computing Analysis > Tel. +44 (0) 1382 86389 > _______________________________________________ > Discuss mailing list > Discuss@compbio.dundee.ac.uk > http://www.compbio.dundee.ac.uk/mailman/listinfo/discuss > ------------------ Geoff Barton, Professor of Bioinformatics, School of Life Sciences University of Dundee, Scotland, UK. geoff@compbio.dundee.ac.uk Tel:+44 1382 385860/345843 (Fax:345764) www.compbio.dundee.ac.uk From tom at compbio.dundee.ac.uk Wed Jan 18 11:50:08 2006 From: tom at compbio.dundee.ac.uk (Tom Walsh) Date: Wed Jan 18 11:50:19 2006 Subject: [Discuss] values.h for stamp mac os x compile In-Reply-To: References: Message-ID: <43CE2B70.5090606@compbio.dundee.ac.uk> Bryan W. Lepore wrote: >please pardon the naive question: i'm trying to use gcc on mac os x to compile >stamp_43, which needs values.h in murzin_P.c: > >gcc -c -g -I. murzin_P.c >murzin_P.c:38:20: values.h: No such file or directory > > I should have CC'd this to the list... The fix for this is to make the following modifications to murzin_P.c: Replace: #include with: #include Replace DMAXEXP on line 116 with DBL_MAX_EXP. Tom From bryanlepore at mail.utexas.edu Sun Jan 22 19:51:20 2006 From: bryanlepore at mail.utexas.edu (Bryan W. Lepore) Date: Sun Jan 22 19:51:21 2006 Subject: [Discuss] stamp manual Message-ID: how would i know if i have the latest greatest stamp manual? i currently have a manual for stamp version 4.3, apparently dated 23 March 1999, as judged by the front page author contact addresses. Prof. Barton sent me the stamp tarball a while ago, and i gathered it was still sort-of in development, so i just wanted to check is all. btw, stamp/alscript compile and run without grief on my powerbook G4 mac os x 10.3.9 w/ gcc 3.3 20030304 (Apple Computer, Inc. build 1495) thanks to the trivial changes in murzin_P.c (values.h -> float.h ; DMAXEXP-> DBL_MAX_EXP) recommended by Tom and Jonathan. -bryan From geoff at compbio.dundee.ac.uk Sun Jan 22 20:46:50 2006 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Sun Jan 22 20:47:02 2006 Subject: [Discuss] stamp manual In-Reply-To: References: Message-ID: Hi Bryan, The manual has not been updated since 4.2, so you have the latest manual. The source for 4.3 should be changed to reflect the new license under which it is distributed, but we have taken ages to get around to doing that. Geoff. On Sun, 22 Jan 2006, Bryan W. Lepore wrote: > how would i know if i have the latest greatest stamp manual? > > i currently have a manual for stamp version 4.3, apparently dated 23 March 1999, > as judged by the front page author contact addresses. > > Prof. Barton sent me the stamp tarball a while ago, and i gathered it was still > sort-of in development, so i just wanted to check is all. > > btw, stamp/alscript compile and run without grief on my powerbook G4 mac os x > 10.3.9 w/ gcc 3.3 20030304 (Apple Computer, Inc. build 1495) thanks to the > trivial changes in murzin_P.c (values.h -> float.h ; DMAXEXP-> DBL_MAX_EXP) > recommended by Tom and Jonathan. > > -bryan > _______________________________________________ > Discuss mailing list > Discuss@compbio.dundee.ac.uk > http://www.compbio.dundee.ac.uk/mailman/listinfo/discuss > ------------------ Geoff Barton, Professor of Bioinformatics, School of Life Sciences University of Dundee, Scotland, UK. geoff@compbio.dundee.ac.uk Tel:+44 1382 385860/345843 (Fax:345764) www.compbio.dundee.ac.uk