[maq-help] Maq compilation problem: incompatible zlib (-lz)

[John O. <joh...@st...>]

I am trying to compile Maq on a 32-bit Linux desktop (Ubuntu Hardy
Heron), using ./configure, make, and make install.  The ./configure
step doesn't give any errors, and reports that zlib.h is present and
usable:

...
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
...

But make stops with error messages that the currently installed libz is
incompatible:

/usr/bin/ld: skipping
incompatible /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../libz.so when
searching for -lz
/usr/bin/ld: skipping
incompatible /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../libz.a when
searching for -lz
/usr/bin/ld: skipping incompatible /usr/bin/../lib/libz.so when
searching for -lz
/usr/bin/ld: skipping incompatible /usr/bin/../lib/libz.a when searching
for -lz
/usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching
for -lz
/usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching
for -lz
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
make[1]: *** [maq] Error 1
make[1]: Leaving directory `/data2/maq/maq-0.7.1'
make: *** [all] Error 2

I searched Ubuntu packages for things with "zlib" or "libz" in the name
or description, and found these:

zlib1g, zlib1g-dev, zlib1g-dbg
zlib-bin, zlibc
libzlcore, libzlcore-dev, libzltext, llibzltext-dev, libzlui-gtk
libzip1, libzip-dev, libzipios++-dev, libzipios++0c2a
libzzip-0-13, libzzip-dev, zziplib-bin
lib64z1, lib64z1-dev

I tried installing all of these except the ones on the last line
(lib64z1, lib64z1-dev), did a make clean, ./configure, and make again,
but still got the same error message (incompatible -lz).  When I
installed lib64z1 and lib64z1-dev, the compilation stopped at the same
step with a different error message, now saying libstdc++ is
incompatible:

/usr/bin/ld: skipping
incompatible /usr/lib/gcc/i486-linux-gnu/4.2.4/libstdc++.so when
searching for -lstdc++
/usr/bin/ld: skipping
incompatible /usr/lib/gcc/i486-linux-gnu/4.2.4/libstdc++.a when
searching for -lstdc++
/usr/bin/ld: skipping
incompatible /usr/lib/gcc/i486-linux-gnu/4.2.4/libstdc++.so when
searching for -lstdc++
/usr/bin/ld: skipping
incompatible /usr/lib/gcc/i486-linux-gnu/4.2.4/libstdc++.a when
searching for -lstdc++
/usr/bin/ld: cannot find -lstdc++
collect2: ld returned 1 exit status
make[1]: *** [maq] Error 1
make[1]: Leaving directory `/data2/maq/maq-0.7.1'
make: *** [all] Error 2

I don't know whether installing lib64z1 solved one problem and now I'm
seeing the second libstdc++ problem, or whether lib64z1 caused the
second problem.  I tested this by installing packages related to
libstdc++, but those didn't help, and a couple of them refused to
install because they would introduce incompatibilities into my system.

Has anyone else had this compilation problem, and is there a known
solution?  I didn't see anything by searching the mail archive.

John Obenauer

--
John C. Obenauer, Ph.D.
Group Leader, Bioinformatics
St. Jude Children's Research Hospital
Mail Stop 312
262 Danny Thomas Place
Memphis, TN 38105-2794
Phone (901)595-3188
Fax (901)595-2945
joh...@st...


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