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Old 08-24-2009, 05:35 AM   #1
RockChalkJayhawk
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Location: Rochester, MN

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Posts: 191
Default Can't make Maq

Hey all,

I have tried to install Maq-0.7.1 from the sourceforge website many times but I see a couple of problems. First I don't think it is configuring right. I keep getting a warning with my zlib.h. Then, it can't findgnu/stubs-64.h.

Any suggestions?

Here is the code:

steven@Home[maq-0.7.1] ./configure [ 8:28AM]
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking if gcc accepts -m64... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... no
checking for sys/stat.h... no
checking for stdlib.h... no
checking for string.h... no
checking for memory.h... no
checking for strings.h... no
checking for inttypes.h... no
checking for stdint.h... no
checking for unistd.h... no
checking zlib.h usability... no
checking zlib.h presence... yes
configure: WARNING: zlib.h: present but cannot be compiled
configure: WARNING: zlib.h: check for missing prerequisite headers?
configure: WARNING: zlib.h: see the Autoconf documentation
configure: WARNING: zlib.h: section "Present But Cannot Be Compiled"
configure: WARNING: zlib.h: proceeding with the preprocessor's result
configure: WARNING: zlib.h: in the future, the compiler will take precedence
checking for zlib.h... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
steven@Home[maq-0.7.1] make [ 8:28AM]
make all-am
make[1]: Entering directory `/home/steven/maq-0.7.1'
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c main.c
In file included from /usr/include/features.h:354,
from /usr/include/stdio.h:28,
from main.c:1:
/usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory
make[1]: *** [main.o] Error 1
make[1]: Leaving directory `/home/steven/maq-0.7.1'
make: *** [all] Error 2
steven@Home[maq-0.7.1] make install [ 8:30AM]
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c main.c
In file included from /usr/include/features.h:354,
from /usr/include/stdio.h:28,
from main.c:1:
/usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory
make: *** [main.o] Error 1
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Old 08-24-2009, 09:44 AM   #2
nilshomer
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Quote:
Originally Posted by RockChalkJayhawk View Post
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c main.c
In file included from /usr/include/features.h:354,
from /usr/include/stdio.h:28,
from main.c:1:
/usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory
make: *** [main.o] Error 1
This could be a number of issues relating to 64-bit computing (you are using a 64-bit processor right?).

Try updating your "libc6-dev" package (c library development package). Also try passing in the option "--disable-multilib" when you run "./configure". Could you tell us what OS and architecture you are using?
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Old 08-24-2009, 10:09 AM   #3
RockChalkJayhawk
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Location: Rochester, MN

Join Date: Mar 2009
Posts: 191
Default

Quote:
Originally Posted by nilshomer View Post
This could be a number of issues relating to 64-bit computing (you are using a 64-bit processor right?).

Try updating your "libc6-dev" package (c library development package). Also try passing in the option "--disable-multilib" when you run "./configure". Could you tell us what OS and architecture you are using?
I am running Bio-Linux on AMD athlon X2 Dual-core QL-64. I tried to update my libc6-dev but when I did, it said I was trying to download the wrong architecture (I was trying the AMD download). Any ideas?
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Old 08-24-2009, 10:22 AM   #4
nilshomer
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Quote:
Originally Posted by RockChalkJayhawk View Post
I am running Bio-Linux on AMD athlon X2 Dual-core QL-64. I tried to update my libc6-dev but when I did, it said I was trying to download the wrong architecture (I was trying the AMD download). Any ideas?
From this page it looks like Bio-Linux likes 32-bit packages only, but their website does not have amazing documentation so I could be wrong. Can you change distributions (I would recommend Ubuntu for a desktop and Cent OS for a server) and install the 64-bit versions?
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Old 08-24-2009, 10:32 AM   #5
RockChalkJayhawk
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Location: Rochester, MN

Join Date: Mar 2009
Posts: 191
Default

Quote:
Originally Posted by nilshomer View Post
From this page it looks like Bio-Linux likes 32-bit packages only, but their website does not have amazing documentation so I could be wrong. Can you change distributions (I would recommend Ubuntu for a desktop and Cent OS for a server) and install the 64-bit versions?
Now it all makes sense! Thanks nilshomer. I will have to change my OS.
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