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megb 07-13-2005 04:05 PM

undefined reference to `__ctype_b_loc'
 
I am a grad student in biology and I am trying to install a program for working with DNA sequences that I downloaded from UC Santa Cruz (inSilico PCR).

Following the instructions provided in the readme after unzipping, I type make in the dir where I unzipped and this is what I get (see below).

Background: I am using my account on a AMD cluster called morpheus at the University of Michigan - I do not know a lot about how it is set up, but according to their website it is running redhat 7.2 or 7.3 (isn't that a bit old?) Maybe the website is just not up to date and it is really a different version, but I do not know how to find out. I did some google searching and saw a lot of references to wrong versions of gcc or glibc with similar errors, but I don't know how to find out what versions I have or how I would change them anyway. So, as you can see, I am very much the newbie, but I would really like to get this program working ASAP.

Thanks for any help.

Meg

cd lib && make
make[1]: Entering directory `/home/mbakewel/isPCR/isPcrSrc/lib'
make[1]: `i386-redhat-linux-gnu/jkweb.a' is up to date.
make[1]: Leaving directory `/home/mbakewel/isPCR/isPcrSrc/lib'
cd jkOwnLib && make
make[1]: Entering directory `/home/mbakewel/isPCR/isPcrSrc/jkOwnLib'
make[1]: `../lib/i386-redhat-linux-gnu/jkOwnLib.a' is up to date.
make[1]: Leaving directory `/home/mbakewel/isPCR/isPcrSrc/jkOwnLib'
cd isPcr && make
make[1]: Entering directory `/home/mbakewel/isPCR/isPcrSrc/isPcr'
cd gfPcr && make
make[2]: Entering directory `/home/mbakewel/isPCR/isPcrSrc/isPcr/gfPcr'
gcc -O -o /home/mbakewel/bin/i386-redhat-linux-gnu/gfPcr gfPcr.o ../../lib/i386-redhat-linux-gnu/jkOwnLib.a ../../lib/i386-redhat-linux-gnu/jkweb.a -lm
../../lib/i386-redhat-linux-gnu/jkOwnLib.a(gfPcrLib.o): In function `upperMatch':
gfPcrLib.o(.text+0x237): undefined reference to `__ctype_toupper_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(axt.o): In function `axtScoreSchemeFromProteinText':
axt.o(.text+0xcdd): undefined reference to `__ctype_b_loc'
axt.o(.text+0xd09): undefined reference to `__ctype_tolower_loc'
axt.o(.text+0xd48): undefined reference to `__ctype_b_loc'
axt.o(.text+0xd78): undefined reference to `__ctype_tolower_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(axt.o): In function `axtAddBlocksToBoxInList':
axt.o(.text+0x131c): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(axt.o): In function `axtIdWithGaps':
axt.o(.text+0x15e8): undefined reference to `__ctype_toupper_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o): In function `differentWord':
common.o(.text+0xad0): undefined reference to `__ctype_toupper_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o): In function `toUpperN':
common.o(.text+0xc97): undefined reference to `__ctype_toupper_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o): In function `toLowerN':
common.o(.text+0xccf): undefined reference to `__ctype_tolower_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o): In function `toggleCase':
common.o(.text+0xd02): undefined reference to `__ctype_b_loc'
common.o(.text+0xd26): undefined reference to `__ctype_tolower_loc'
common.o(.text+0xd2d): undefined reference to `__ctype_b_loc'
common.o(.text+0xd45): undefined reference to `__ctype_toupper_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o): In function `touppers':
common.o(.text+0xd78): undefined reference to `__ctype_toupper_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o): In function `tolowers':
common.o(.text+0xed9): undefined reference to `__ctype_tolower_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o): In function `chopByWhite':
common.o(.text+0x10b9): undefined reference to `__ctype_b_loc'
common.o(.text+0x10ec): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o): In function `skipLeadingSpaces':
common.o(.text+0x117f): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o): In function `skipToSpaces':
common.o(.text+0x11c4): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o): In function `eraseTrailingSpaces':
common.o(.text+0x1208): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o)(.text+0x1247): more undefined references to `__ctype_b_loc' follow
../../lib/i386-redhat-linux-gnu/jkweb.a(common.o): In function `strstrNoCase':
common.o(.text+0x1b8a): undefined reference to `__ctype_tolower_loc'
common.o(.text+0x1bb3): undefined reference to `__ctype_tolower_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(dnaseq.o): In function `maskFromUpperCaseSeq':
dnaseq.o(.text+0x377): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(dnautil.o): In function `initNtVal':
dnautil.o(.text+0x18): undefined reference to `__ctype_b_loc'
dnautil.o(.text+0x81): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(dnautil.o): In function `lookupCodon':
dnautil.o(.text+0x35a): undefined reference to `__ctype_toupper_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(dnautil.o): In function `upperToN':
dnautil.o(.text+0x919): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(dnautil.o): In function `lowerToN':
dnautil.o(.text+0x95d): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(dnautil.o): In function `initAaVal':
dnautil.o(.text+0xc69): undefined reference to `__ctype_tolower_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(fa.o): In function `faReadMixedNext':
fa.o(.text+0x198): undefined reference to `__ctype_b_loc'
fa.o(.text+0x210): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(fa.o): In function `faNextSeqFromMemText':
fa.o(.text+0x3c2): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(fa.o): In function `faFastReadNext':
fa.o(.text+0x66f): undefined reference to `__ctype_b_loc'
fa.o(.text+0x6cd): undefined reference to `__ctype_b_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(fa.o)(.text+0x937): more undefined references to `__ctype_b_loc' follow
../../lib/i386-redhat-linux-gnu/jkweb.a(wildcmp.o): In function `subMatch':
wildcmp.o(.text+0x15): undefined reference to `__ctype_toupper_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(wildcmp.o): In function `wildMatch':
wildcmp.o(.text+0xd1): undefined reference to `__ctype_toupper_loc'
../../lib/i386-redhat-linux-gnu/jkweb.a(internet.o): In function `internetIsDottedQuad':
internet.o(.text+0x9): undefined reference to `__ctype_b_loc'
internet.o(.text+0x49): undefined reference to `__ctype_b_loc'
collect2: ld returned 1 exit status
make[2]: *** [gfPcr] Error 1
make[2]: Leaving directory `/home/mbakewel/isPCR/isPcrSrc/isPcr/gfPcr'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/mbakewel/isPCR/isPcrSrc/isPcr'
make: *** [all] Error 2

This is the listing in the dir where I am trying to make:
-rw-rw-r-- 1 mbakewel users 1309 Sep 1 2004 README
-rw-rw-r-- 1 mbakewel users 244 Oct 15 2004 foo
drwxrwxr-x 4 mbakewel users 4096 Dec 8 2004 gfServer
drwxrwxr-x 3 mbakewel users 4096 Jul 13 15:11 inc
drwxrwxr-x 6 mbakewel users 4096 Jul 13 15:05 isPcr
drwxrwxr-x 5 mbakewel users 4096 Dec 8 2004 jkOwnLib
drwxrwxr-x 9 mbakewel users 8192 Jul 13 14:35 lib
-rw-rw-r-- 1 mbakewel users 81 Sep 1 2004 makefile

leonscape 07-13-2005 04:44 PM

It does appear to be some fundamental stuff that's missing. Which is very odd. I think you might be better off talking to the people that administer the system. Maybe there development headers are out of sync with the actual libs on the system.

megb 07-13-2005 05:14 PM

I have actually gotten some other stuff to work on this same system - other programs I also downloaded from the same source - but in the past, I have just followed the install instructions (unzip, type make...) and everything just worked - not sure if that is pertinent to the present situation. Thanks again.

Meg

leonscape 07-13-2005 05:17 PM

Hmm, it maybe just a bad source, try typing make in the sub folders first ( some might be needed to compile before others ). Then do a make in the root again.


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