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

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.

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

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.