Help - MAQ getting started

[inesdesantiago]

Hello
I am trying to install maq in a 32-bit ubuntu. I will only run small files, so 32-bit is OK for me.
However i have a problem with the ./configure; make; make install
Can some one help me? here is what I have:

isantiago@isantiago:/usr/local/maq-0.7.1$ ./configure
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... no
checking for zlib.h... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged

isantiago@isantiago:/usr/local/maq-0.7.1$ make
make all-am
make[1]: Entering directory `/usr/local/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 `/usr/local/maq-0.7.1'
make: *** [all] Error 2

isantiago@isantiago:/usr/local/maq-0.7.1$ sudo make install
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

thanks!
regards

[andpet]

Help - MAQ getting started

Hi,

currently you are trying to compile maq in 64 bit (look for the -m64 in the output of make). Since you don't have a 64 bit operating system the compiler doesn't find the neccessary libraries (stubs-64.h). Try one of two ways to fix that:

1)
make clean
set the environment variable CC to "gcc -m32" (I assume gcc is your compiler,)
./configure
make

2)
make clean
edit the file Makefile.generic and look for CFLAGS; change -m64 into -m32
make -f Makefile.generic

This sets the -m32 flag and tells the compiler to build the 32 bit version.

greets,

Andreas

[inesdesantiago]

working MAQ 32bit

I guess it is working now!
The manual is not very clear!

Thanks
Ines

[baozhi]

I had the same problem, tried changing -m64 to -m32 in Makefile.generic, got another error:
"/usr/bin/ld: i386:x86-64 architecture of input file 'const.o' is incompatible with i386 output."

I have been struggling on it for a while, please help!!!

[andpet]

Hi,

I assume before changing -m64 to -m32 you tried to compile the 64-bit version of maq ?

To me it seems that the file const.o (a part of the maq program) is still a 64-bit version and you can't combine parts of different architectures to build maq.

Have you done 'make clean' before compiling the 32 bit version ? Just to be sure look for all files that have the ending *.o and delete them. Then try again ...

greets,

Andreas

[baozhi]

Did a "make clean", worked perfectly. Thanks a million. :-)

[Ender985]

Hello,

I'm also trying to install Maq, but even though after cleaning I editied Makefile.generic -m64 to -m32,

CFLAGS=		-g -Wall -O2 -m32

it seems the installer is still trying to give me the 64 bit version. Everything works fine until it reaches this point:

make[1]: Entering directory `/home/Downloads/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/Downloads/maq-0.7.1'
make: *** [all] Error 2
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

I tried to figure out where is this -m64 call coming from but I can't seem to find it. Any suggestions?


Thanks!

[inesdesantiago]

I think you are trying to run the ./configure; make; make install (?).
However, when you edit the Makefile.generic like you did you have to do the installation differently.
That is, after editing the Makefile.generic file you JUST have to type:

make clean
make -f Makefile.generic

After this, the installation should work now..
Then, you need to manually move the three executable files that were generated (`maq', `maq.pl' and `farm-run.pl') to the destination directory (the default destination directory is normally /usr/local/bin)

[Ender985]

In the end, after following your advice and also getting the zlib1g-dev package (as some zlib.h was missing), it seems I was able to successfully install. I was exactly trying to run $ ./configure; make; make install , I wasn't aware that I should use the other installation method, as I'm fairly new to Linux.

Thanks a lot!

[Ender985]

Sorry - double post

[mandova]

Hi,

I assume before changing -m64 to -m32 you tried to compile the 64-bit version of maq ?

To me it seems that the file const.o (a part of the maq program) is still a 64-bit version and you can't combine parts of different architectures to build maq.

Have you done 'make clean' before compiling the 32 bit version ? Just to be sure look for all files that have the ending *.o and delete them. Then try again ...

greets,

Andreas

Hi~It is very useful to see these posts a year ago, since I encountered the same problem(for a while...) I did what you said (change to -m32)and a "make clean", then"make -f Makefile.generic", still "stubs-64.h: no such file..."; I deleted the const.o and tried again, still that message...
Before that I tried to install libc6-dev-amd64 which contains in its list /usr/include/gnu/stubs-64.h
but it gave me something like "can't fetch....403 forbidden"
Is it that hard?!...I reinstalled my computer for this software...

[mandova]

In the end, after following your advice and also getting the zlib1g-dev package (as some zlib.h was missing), it seems I was able to successfully install. I was exactly trying to run $ ./configure; make; make install , I wasn't aware that I should use the other installation method, as I'm fairly new to Linux.

Thanks a lot!

I wonder why this wouldn't work for me...

[mandova]

solved at last!!

I'd like thank all that inspired me...I changed win vista to Ubuntu's hardy(32 bit system) to run MAQ, after I changed my software sources to sjtu's, and installed libc-dev-amd64 for stubs-64.h, and zliblg-dev for zlib.h, it finally appears that "make" succeeded!