Problem with stral installation

[Marcin Sajek]

I try to install stral and after installing all dependencies I have the following error after 'make':

stral.o: In function main': /home/marcin/Downloads/stral/stral.c:422: undefined reference to rpl_malloc'
/home/marcin/Downloads/stral/stral.c:423: undefined reference to rpl_malloc' /home/marcin/Downloads/stral/stral.c:453: undefined reference to rpl_malloc'
iofuncs.o: In function recursion': /home/marcin/Downloads/stral/iofuncs.c:610: undefined reference to rpl_malloc'
/home/marcin/Downloads/stral/iofuncs.c:611: undefined reference to rpl_malloc' iofuncs.o:/home/marcin/Downloads/stral/iofuncs.c:748: more undefined references to rpl_malloc' follow
iofuncs.o: In function parsenewicktree': /home/marcin/Downloads/stral/iofuncs.c:436: undefined reference to rpl_realloc'
iofuncs.o: In function printdistmatrix': /home/marcin/Downloads/stral/iofuncs.c:204: undefined reference to rpl_malloc'
iofuncs.o: In function readfromprobfile': /home/marcin/Downloads/stral/iofuncs.c:112: undefined reference to rpl_malloc'
/home/marcin/Downloads/stral/iofuncs.c:140: undefined reference to rpl_malloc' iofuncs.o: In function print2probfile':
/home/marcin/Downloads/stral/iofuncs.c:50: undefined reference to rpl_malloc' iofuncs.o: In function remgaps':
/home/marcin/Downloads/stral/iofuncs.c:323: undefined reference to rpl_realloc' part_func.o: In function mysprintf_bppm':
/home/marcin/Downloads/stral/part_func.c:901: undefined reference to
rpl_malloc' collect2: ld returned 1 exit status make[1]: *** [stral] Error 1 make[1]: Leaving directory /home/marcin/Downloads/stral'
make: *** [install-recursive] Error 1

I try to use:
ac_cv_func_malloc_0_nonnull=yes
ac_cv_func_realloc_0_nonnull=yes
before ./configure
but it doesn't work

I did it in 32 bit Ubuntu 10.04. In the newer versions, I am not able to compile ViennaRNA-1.8.5.

I will be grateful for any suggestions

Marcin

[Andreas Wilm]

Hi Marcin, I just successfully compiled Stral on my Ubuntu machine. There must be something missing on yours. There are two things you can try: 1. sudo apt-get install build-essential 2. Removing the lines containing AC_FUNC_MALLOC and AC_FUNC_REALLOC in the configure.ac and then rerun ./bootstrap In either case, run ./configure and make again Regarding installation of the dependencies, try the following: *ViennaRNA* I installed ViennaRNA with conda: conda install viennarna=1.8 *Squid:* wget -nd http://eddylab.org/software/squid/squid-1.9g.tar.gz tar xvzf squid-1.9g.tar.gz cd squid-1.9g/ ./configure make sudo make install *mhash* wget -nd ' https://downloads.sourceforge.net/project/mhash/mhash/0.9.9.9/mhash-0.9.9.9.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fmhash%2Ffiles%2Fmhash%2F0.9.9.9%2Fmhash-0.9.9.9.tar.gz%2Fdownload&ts=1609806714' -Omhash-0.9.9.9.tar.gz tar xvzf mhash-0.9.9.9.tar.gz cd mhash-0.9.9.9/ ./configure make sudo make install Let me know how it went. Best, Andreas

…

On Mon, 4 Jan 2021 at 23:56, MSajek ***@***.***> wrote: I try to install stral and after installing all dependencies I have the following error after 'make': stral.o: In function main': /home/marcin/Downloads/stral/stral.c:422: undefined reference to rpl_malloc' /home/marcin/Downloads/stral/stral.c:423: undefined reference to rpl_malloc' /home/marcin/Downloads/stral/stral.c:453: undefined reference to rpl_malloc' iofuncs.o: In function recursion': /home/marcin/Downloads/stral/iofuncs.c:610: undefined reference to rpl_malloc' /home/marcin/Downloads/stral/iofuncs.c:611: undefined reference to rpl_malloc' iofuncs.o:/home/marcin/Downloads/stral/iofuncs.c:748: more undefined references to rpl_malloc' follow iofuncs.o: In function parsenewicktree': /home/marcin/Downloads/stral/iofuncs.c:436: undefined reference to rpl_realloc' iofuncs.o: In function printdistmatrix': /home/marcin/Downloads/stral/iofuncs.c:204: undefined reference to rpl_malloc' iofuncs.o: In function readfromprobfile': /home/marcin/Downloads/stral/iofuncs.c:112: undefined reference to rpl_malloc' /home/marcin/Downloads/stral/iofuncs.c:140: undefined reference to rpl_malloc' iofuncs.o: In function print2probfile': /home/marcin/Downloads/stral/iofuncs.c:50: undefined reference to rpl_malloc' iofuncs.o: In function remgaps': /home/marcin/Downloads/stral/iofuncs.c:323: undefined reference to rpl_realloc' part_func.o: In function mysprintf_bppm': /home/marcin/Downloads/stral/part_func.c:901: undefined reference to rpl_malloc' collect2: ld returned 1 exit status make[1]: *** [stral] Error 1 make[1]: Leaving directory /home/marcin/Downloads/stral' make: *** [install-recursive] Error 1 I try to use: ac_cv_func_malloc_0_nonnull=yes ac_cv_func_realloc_0_nonnull=yes before ./configure but it doesn't work I did it in 32 bit Ubuntu 10.04. In the newer versions, I am not able to compile ViennaRNA-1.8.5. I will be grateful for any suggestions Marcin — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAILSCP2366CPBH33WGCTXDSYHQLZANCNFSM4VTGOIVA> .

-- Andreas Wilm [e-mail] | 0x7C68FBCC

[Andreas Wilm]

Forgot that I keep a copy of the third party libraries in the third-party folder. Just use them, rather then downloading or installing via conda.

[Marcin Sajek]

Hi Andreas,
Thanks for the very fast answer. I hashed the lines containing AC_FUNC_MALLOC and AC_FUNC_REALLOC in the
configure.ac and rerun ./bootstrap, ./configure and make and everything is ok. I finished the installation (sudo make install) and after running stral the following error occurs:
error while loading shared libraries: libmhash.so.2: cannot open shared object file: No such file or directory
I fixed it using:
sudo ldconfig -v
and everything works fine!
Thanks a lot!

[Andreas Wilm]

Wonderful. Thanks for reporting back