Compiling slr ...ERROR

[leobi...@gmail.com]

Hello!
I'm using ETE toolkit and now I would like to mesure the king of pressure is affectig the aminoacids of my aminoacid sequences so I need the SLR program working.
I'm having a compilation error when run the "ete3 upgrade-external-tools" command.

user@machine:~$ ete3 upgrade-external-tools

Downloading latest version of tools...
Decompressing...
Compiling tools...
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/trimal
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/multi2hat3s
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/pmodeltest.py
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/dialign-tx
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/dndfast7
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/countlen
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/pairlocalalign
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/sextet5
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/randrep
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/replaceu
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/catrep
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/regtable2seq
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/consel
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/probcons
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/tbfast
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/catpv
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/rnatest
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/dndblast
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/disttbfast
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/raxmlHPC-PTHREADS-SSE3
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/clustalo
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/catass
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/t_coffee
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/statal
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/makerep
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/mafft
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/catmt
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/kalign
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/setcore
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/makermt
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/dndpre2
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/dndpre
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/FastTree
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/splittbfast
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/mafft-profile
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/pair2hat3s
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/phyml
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/prank
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/restoreu
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/getlag
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/dialigntx_conf
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/readal
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/score
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/treeass
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/mafft.1
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/mccaskillwrap
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/seqmt
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/seq2regtable
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/mafft-distance
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/contrafoldwrap
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/codeml
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/mafft-homologs.1
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/f2cl
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/mafft-homologs.rb
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/dvtditr
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/raxmlHPC-SSE3
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/pairash
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/muscle
cleaning /home/leomad/.etetoolkit/ext_apps-latest/bin/catci
Compiling tcoffee ...Ok
Compiling clustalo ...argtable2 library is missing. Attempting to compile a local version
Ok
Compiling muscle ...Ok
Compiling dialigntx ...Ok
Compiling mafft ...Ok
Compiling kalign ...Ok
Compiling prank ...Ok
Compiling probcons ...Ok
Compiling trimal ...Ok
Compiling pmodeltest ...Ok
Compiling fasttree ...Ok
Compiling raxml ...Ok
Compiling phyml ...Ok
Compiling consel ...Ok
Compiling paml ...Ok
Compiling slr ...ERROR
Compiling slr. Check log /home/leomad/.etetoolkit/ext_apps-latest/slr.log



The slr.log file is the following:


rm: cannot remove ‘/home/leomad/.etetoolkit/ext_apps-latest/bin/Slr’: No such file or directory
rm -f *~ *.o
rm: cannot remove ‘../bin/Slr’: No such file or directory
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o slr.o -c slr.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o like.o -c like.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o tree.o -c tree.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o data.o -c data.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o rng.o -c rng.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o model.o -c model.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o bases.o -c bases.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o codonmodel.o -c codonmodel.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o gencode.o -c gencode.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o utility.o -c utility.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o matrix.o -c matrix.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o optimize_new.o -c optimize_new.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o spinner.o -c spinner.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o options.o -c options.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o tree_data.o -c tree_data.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o linemin.o -c linemin.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o gamma.o -c gamma.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o statistics.o -c statistics.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o mystring.o -c mystring.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o nucmodel.o -c nucmodel.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o root.o -c root.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o vec.o -c vec.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o brent.o -c brent.c
gcc -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -o rbtree.o -c rbtree.c
gcc -o ../bin/Slr slr.o like.o tree.o data.o rng.o model.o bases.o codonmodel.o gencode.o utility.o matrix.o optimize_new.o spinner.o options.o tree_data.o linemin.o gamma.o statistics.o mystring.o nucmodel.o root.o vec.o brent.o rbtree.o -O4 -fomit-frame-pointer -funroll-loops -DNDEBUG -std=gnu99 -L -lblas -llapack -lm
/usr/bin/ld: matrix.o: undefined reference to symbol 'dgemm_'
//usr/lib/libblas.so.3: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make: *** [Slr] Error 1
cp: cannot stat ‘../bin/Slr’: No such file or directory
ls: cannot access /home/leomad/.etetoolkit/ext_apps-latest/bin/Slr: No such file or directory



I have the same problem when I download the software from 'http://www.ebi.ac.uk/goldman-srv/SLR/#download' and run the "make" command.

I have no idea how to solve this issue. Please help me.
Thank you!

[Jaime Huerta Cepas]

SLR is hard to compile. Most probably you are missing some math libraries in your system. 

ETE provides precompiled versions of all tools through a conda package. If you install ete as explained in http://etetoolkit.org/download/, you should get a fully working copy in a few minutes. That's the easiest way IMO.

 

 

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[Renato Alves]

On 07/11/16 17:36, Jaime Huerta Cepas wrote:
> SLR is hard to compile. Most probably you are missing some math libraries in your system.
> ETE provides precompiled versions of all tools through a conda package. If you install ete as explained in http://etetoolkit.org/download/, you should get a fully working copy in a few minutes. That's the easiest way IMO.
>

> /usr/bin/ld: matrix.o: undefined reference to symbol 'dgemm_'
> //usr/lib/libblas.so.3: error adding symbols: DSO missing from command line

Jaime is right about the missing libraries.

If you google the error above you will find that "dgemm_" is part of a math library called LAPACK.
You'll have to install it to compile SLR or use the conda setup as suggested by Jaime.

Cheers,
Renato

[dsalaz...@gmail.com]

I had the same issue on my machine (Fedora 21, 32 bits) and I had both blas and lapack properly installed on my machine. After a quick search I found this on Stack Overflow[1]:

>So you have to put first the -L/directory/of/the/library so the compiler is
>aware of the directory containing your library, and then the -llibrary flag.

So, my hacky solution was:

0) Check "whereis liblapack" and "whereis libblas" and see where your libraries are located. I found "usr/lib/liblapack.a" and "usr/lib/libblas.a"respectively.

1) Run $ete3 upgrade-external-tools
2) Define a target directory (in my case: /media/my_drive/etetoolkit/ )
3) While the instalation is running, open etetoolkit/ext_apps-latest/src/slr/src/Makefile.linux (I'm assuming you're using a linux distro) and modify this line:

>LDFLAGS = -L$(BLASDIR) -lblas -llapack -lm

to:

>LDFLAGS = -L/usr/lib/lapack -llapack -L/usr/lib/libblas -lblas -lm

In other words, tell the compiler where your libraries are located. If you do this in the right way, the installation will end with no problems.

Greetings!




[1] http://stackoverflow.com/questions/20669410/gfortran-lapack-undefined-reference-error