Error during compilation of vamos

[dbeyter]

Hi,
While runnning "make" in the following step:
wget https://github.com/ChaissonLab/vamos/archive/refs/tags/vamos-v1.1.0.tar.gz
tar -zxvf vamos-v1.1.0.tar.gz
cd vamos-v1.1.0/src; make

I received the following error while being in the vamos environment created using conda and installing the 3 packages given in the requirements.txt file:

/home/dorukb/gcc_installations/gcc-8.3.0_bin/bin/g++ -std=c++17 -O3 -DNDEBUG -c main.cpp -I /home/dorukb/.conda/envs/vamos/include
/home/dorukb/gcc_installations/gcc-8.3.0_bin/bin/g++ -std=c++17 -O3 -DNDEBUG -c io.cpp -I /home/dorukb/.conda/envs/vamos/include -I ../abPOA-1.2.5/include -I /home/dorukb/.conda/envs/vamos/include
/home/dorukb/gcc_installations/gcc-8.3.0_bin/bin/g++ -std=c++17 -O3 -DNDEBUG -c vcf.cpp -I /home/dorukb/.conda/envs/vamos/include
/home/dorukb/gcc_installations/gcc-8.3.0_bin/bin/g++ -std=c++17 -O3 -DNDEBUG -c vntr.cpp -I ../abPOA-1.2.5/include -I ../alglib/src -I ../edlib/include -I /home/dorukb/.conda/envs/vamos/include
/home/dorukb/gcc_installations/gcc-8.3.0_bin/bin/g++ -std=c++17 -O3 -DNDEBUG -c acc_lookup_table.cpp -I ../alglib/src -I ../edlib/include -I ../abPOA-1.2.5/include -I /home/dorukb/.conda/envs/vamos/include
/home/dorukb/gcc_installations/gcc-8.3.0_bin/bin/g++ -std=c++17 -O3 -DNDEBUG -c phase.cpp -I /home/dorukb/.conda/envs/vamos/include
/home/dorukb/gcc_installations/gcc-8.3.0_bin/bin/g++ -std=c++17 -O3 -DNDEBUG -c msa.cpp -I ../abPOA-1.2.5/include
/home/dorukb/gcc_installations/gcc-8.3.0_bin/bin/g++ -std=c++17 -O3 -DNDEBUG -o vamos main.o io.o vcf.o vntr.o acc_lookup_table.o phase.o msa.o -L /home/dorukb/.conda/envs/vamos/lib -lhts -lz -lpthread -labpoa -L ../static_lib/ -lalglib -ledlib -lrt
/usr/bin/ld: warning: libdeflate.so.0, needed by /home/dorukb/.conda/envs/vamos/lib/libhts.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libbz2.so.1.0, needed by /home/dorukb/.conda/envs/vamos/lib/libhts.so, not found (try using -rpath or -rpath-link)
/home/dorukb/.conda/envs/vamos/lib/libhts.so: undefined reference to libdeflate_free_compressor' /home/dorukb/.conda/envs/vamos/lib/libhts.so: undefined reference to libdeflate_deflate_decompress'
/home/dorukb/.conda/envs/vamos/lib/libhts.so: undefined reference to libdeflate_alloc_compressor' /home/dorukb/.conda/envs/vamos/lib/libhts.so: undefined reference to BZ2_bzBuffToBuffCompress'
/home/dorukb/.conda/envs/vamos/lib/libhts.so: undefined reference to libdeflate_gzip_decompress' /home/dorukb/.conda/envs/vamos/lib/libhts.so: undefined reference to libdeflate_free_decompressor'
/home/dorukb/.conda/envs/vamos/lib/libhts.so: undefined reference to BZ2_bzBuffToBuffDecompress' /home/dorukb/.conda/envs/vamos/lib/libhts.so: undefined reference to libdeflate_crc32'
/home/dorukb/.conda/envs/vamos/lib/libhts.so: undefined reference to libdeflate_deflate_compress' /home/dorukb/.conda/envs/vamos/lib/libhts.so: undefined reference to libdeflate_gzip_compress'
/home/dorukb/.conda/envs/vamos/lib/libhts.so: undefined reference to `libdeflate_alloc_decompressor'
collect2: error: ld returned 1 exit status
make: *** [vamos] Error 1

Here are the packages and their versions conda installed:

Downloading and Extracting Packages
libdeflate-1.13 | 79 KB
libopenblas-0.3.21 | 10.1 MB
numpy-1.23.4 | 7.1 MB
liblapack-3.9.0 | 13 KB
htslib-1.16 | 2.3 MB
python-3.10.6 | 29.0 MB
libcblas-3.9.0 | 13 KB
boost-cpp-1.80.0 | 17.4 MB
abpoa-1.2.5 | 161 KB
boost-1.80.0 | 350 KB
libblas-3.9.0 | 13 KB
libgfortran-ng-12.2. | 22 KB
libgfortran5-12.2.0 | 1.8 MB
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

I would be happy if you can help with the error I am seeing above.
Thank you,
Doruk

[Jingwen7]

Hi Doruk,

Thanks for reporting this error!

We cannot replicate this error on our end. I doubt this error is a conda solver issue. So the conda solver installed libdeflate and libbz2 of the wrong version in your env. To solve this, can you try the following?

1. recreate a conda env with specified libbz2 version: conda create --name vamos_test python=3.10 bzip2=1.0.8
2. reinstall requirements with a specified libdeflate version: conda install -c bioconda libdeflate=1.7 htslib=1.13 abpoa=1.2.5 boost=1.73.0
3. then remake to see if the error goes away.

Best,
Jingwen

[dbeyter]

Hi Jingwen,

I applied the changes you suggested, though the same error remained. It seemed like a linking problem, so per https://github.com/samtools/htslib/issues/688 I added " -Wl,-R$(CONDA_PREFIX)/lib" into the rule of vamos in the Makefile, and I was to create the vamos executable.

So the edited Makefile I am using has the vamos rule as:

vamos: main.o io.o vcf.o vntr.o acc_lookup_table.o phase.o msa.o
        $(CXX) $(CFLAGS) -o $@ $^ -L $(CONDA_PREFIX)/lib -Wl,-R$(CONDA_PREFIX)/lib   $(LIBS) -L ../static_lib/ -lalglib -ledlib -lrt

On a side note, and for reference: To be able to run anything that uses conda, I need to use conda-pack to pack/zip a conda environment to carry it to another machine with restricted or no internet access. I noticed I was not able to do this for any environment with python >= 3.10, so I used python 3.9 for the vamos conda env and used the requirements.txt file as is. I was fortunately still able to create the vamos executable. I managed to run the sample command you provided, with the demo.aln.bam file.

I left the issue open in case you wanted to comment on anything that may be erroneous in the workaround I provided, otherwise feel free to close it!

Thank you!
Doruk