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ratschlab / rDiff

Tests for Differential RNA Isoform Expression
GNU General Public License v3.0
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Error while 'make' #3

Closed teresouza closed 9 years ago

teresouza commented 9 years ago

Hi, I was trying to install rDiff but I keep getting this error while running make:

[...] gcc -c -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/octave-3.8.2/octave/.. -I/usr/include/octave-3.8.2/octave -I/usr/include/hdf5/serial -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -g -I. liblfev.c -o liblfev.o liblfev.c: In function ‘getnextdir’: liblfev.c:4233:3: warning: zero-length gnu_printf format string [-Wformat-zero-length] { sprintf(dirnext,""); ^ g++ -shared -Wl,-Bsymbolic -o mexpp.mex mexpp.o mlfut.o liblocf.o libmut.o libtube.o liblfev.o -L/usr/lib/x86_64-linux-gnu/octave/3.8.2 -L/usr/lib/x86_64-linux-gnu -loctinterp -loctave -Wl,-Bsymbolic-functions -Wl,-z,relro
cp mexpp.mex ../mex/ make[1]: Leaving directory '/home/terezinha/Downloads/rDiff/src/locfit/Source'

I used ./configure -i to set up paths and everything seems ok, so what seems to be the problem? Thanks!

vipints commented 9 years ago

what is the underlying operating system here?

teresouza commented 9 years ago

Ubuntu 15.04 x64. I also tried to run through galaxy (locally, adding to my tool shed as admin), specifying paths and all in the rdiff_config.sh, but it also ended in an error. Apparently it cannot start octave - which appears to be the same problem as above since it cannot generate some mex files. This was the last error:

error: get_reads_for_gene: /home/terezinha/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/rdiff/29a698dc5c7e/rdiff/rDiff/src/tools/read_utils/get_reads.mex: failed to load: libcruft.so: cannot open shared object file: No such file or directory error: ca

This was at the end of the log: [...] starting Octave failed

And I tried several times to re-'make' but after the first failed attempt I get this: cd rDiff make echo Entering ./mex Entering ./mex cd mex ; make octave make[1]: Entering directory '/home/terezinha/Downloads/rDiff/mex' make[1]: Nothing to be done for 'octave'. make[1]: Leaving directory '/home/terezinha/Downloads/rDiff/mex' echo Entering ./src/locfit/Source Entering ./src/locfit/Source cd src/locfit/Source ; make octave make[1]: Entering directory '/home/terezinha/Downloads/rDiff/src/locfit/Source' make[1]: Nothing to be done for 'octave'. make[1]: Leaving directory '/home/terezinha/Downloads/rDiff/src/locfit/Source'

So I guess the problem here is octave, then? What should I do? Thanks!

vipints commented 9 years ago

Using the guide https://www.gnu.org/software/octave/doc/interpreter/Compiling-Octave-with-64_002dbit-Indexing.html, we have automated the process of compiling the octave 64bit and you can get it from here: https://github.com/vipints/oqtans/blob/master/oqtans_src/octave-3.6.4_x64.tar.bz2

vipints commented 9 years ago

As you saw already this is also nicely documented in #2