Installation Error for SuperReads

sum732 commented 4 years ago

Hi, I was able to build and install stringtie. However, when I am trying to install SuperRead. I given following error messages. Please suggest how to fix the issues

SuperReadsR/gtest.mk:15: library used but `RANLIB' is undefined
SuperReadsR/gtest.mk:15:   The usual way to define `RANLIB' is to add `AC_PROG_RANLIB'
SuperReadsR/gtest.mk:15:   to `configure.ac' and run `autoconf' again.
SuperReadsR/Makefile.am:188:   `SuperReadsR/gtest.mk' included from here
jellyfish/gtest.mk:5: Libtool library used but `LIBTOOL' is undefined
jellyfish/gtest.mk:5:   The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL'
jellyfish/gtest.mk:5:   to `configure.ac' and run `aclocal' and `autoconf' again.
jellyfish/gtest.mk:5:   If `AC_PROG_LIBTOOL' is in `configure.ac', make sure
jellyfish/gtest.mk:5:   its definition is in aclocal's search path.
jellyfish/Makefile.am:216:   `jellyfish/gtest.mk' included from here
quorum/gtest.mk:5: Libtool library used but `LIBTOOL' is undefined
quorum/gtest.mk:5:   The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL'
quorum/gtest.mk:5:   to `configure.ac' and run `aclocal' and `autoconf' again.
quorum/gtest.mk:5:   If `AC_PROG_LIBTOOL' is in `configure.ac', make sure
quorum/gtest.mk:5:   its definition is in aclocal's search path.
quorum/Makefile.am:111:   `quorum/gtest.mk' included from here
autoreconf: automake failed with exit status: 1

Autoconf/2.69-goolf-1.4.10 is in path as mentioned. It looks like that some library is needed and its not able to find. While building StringTie required GCC compiler was loaded all went fine.

Thanks!

sum732 commented 4 years ago

Got it resolved. Some GCC libraries were not available. In the module. Changes the appropriate module and it worked out.

V-JJ commented 1 year ago

Hello!

We have managed to partially solve the same problem by installing libtool. However, the following error keeps rising. It is related somehow with swig and jellyfish. By the way, it also happened when we tried to install masurca from source code. The installation of swig didn't solve the problem.

Here is the error. Any help would be appreciated (with some detailed explanation please :) )

[...]
swig/perl5/swig_wrap.cpp:322:10: fatal error: string.h: No such file or directory
  322 | #include <string.h>
      |          ^~~~~~~~~~
compilation terminated.
make[2]: *** [Makefile:1656: swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1/jellyfish'
make[1]: *** [Makefile:2435: install] Error 2
make[1]: Leaving directory '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1/jellyfish'
Making install in ufasta pwd /media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1
make[1]: Entering directory '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1/ufasta'
make  install-am
make[2]: Entering directory '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1/ufasta'
make[3]: Entering directory '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1/ufasta'
make[3]: Nothing to be done for 'install-data-am'.
 /usr/bin/mkdir -p '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c ufasta '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/bin'
libtool: install: /usr/bin/install -c ufasta /media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/bin/ufasta
make[3]: Leaving directory '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1/ufasta'
make[2]: Leaving directory '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1/ufasta'
make[1]: Leaving directory '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1/ufasta'
Making install in quorum pwd /media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1
make[1]: Entering directory '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1/quorum'
make  install-am
make[2]: Entering directory '/media/raul/DiscDur/Programs/stringtie-2.2.1/SuperReads_RNA/global-1/quorum'
  CXX      src/error_correct_reads.o
  CXX      src/create_database.o
  CXX      src/merge_mate_pairs.o
  CXX      src/split_mate_pairs.o
src/create_database.cc:23:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory
   23 | #include <jellyfish/mer_dna.hpp>
      |          ^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [Makefile:931: src/create_database.o] Error 1
make[2]: *** Waiting for unfinished jobs....
src/merge_mate_pairs.cc:4:10: fatal error: jellyfish/stream_manager.hpp: No such file or directory
    4 | #include <jellyfish/stream_manager.hpp>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [Makefile:931: src/merge_mate_pairs.o] Error 1
src/error_correct_reads.cc:25:10: fatal error: jellyfish/atomic_gcc.hpp: No such file or directory
   25 | #include <jellyfish/atomic_gcc.hpp>

[...]

Thanks,

gpertea / stringtie

Installation Error for SuperReads #280