Installation error

[aserres]

Hi,

Thank you for your contribution with SViper, we are trying to apply it to polish structural variants called using ONT in humans.

I'm encountering an error trying to install SViper in a slurm/lustre cluster system. Note that my GCC version (6.3.0) is not the recommended, but I do not have access to another. Could that be the cause of the problem? I'd welcome any input to try to fix the issue.

Attached is the full error report:

[aserres@login1 build]$ cmake ../
-- The CXX compiler identification is GNU 6.3.0
-- Check for working CXX compiler: /apps/GCC/6.3.0/bin/c++
-- Check for working CXX compiler: /apps/GCC/6.3.0/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
source dir: /scratch/devel/aserres/bin/SViper
-- These dependencies were found:
OPENMP TRUE -fopenmp
ZLIB TRUE 1.2.3
SEQAN TRUE 2.4.0
-- The requirements were met.
-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/devel/aserres/bin/SViper/build
[aserres@login1 build]$ make sviper
Scanning dependencies of target sviper
[ 50%] Building CXX object CMakeFiles/sviper.dir/src/sviper.cpp.o
In file included from /scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic.h:101:0,
from /scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/bam_io.h:46,
from /scratch/devel/aserres/bin/SViper/include/sviper/basics.h:9,
from /scratch/devel/aserres/bin/SViper/include/sviper/auxiliary.h:2,
from /scratch/devel/aserres/bin/SViper/include/sviper/io.h:7,
from /scratch/devel/aserres/bin/SViper/src/sviper.cpp:1:
/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h: In function ‘bool sviper::polish_variant(sviper::Variant&, sviper::input_output_information&)’:
/scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘viewRecords’ is not a member of ‘seqan’
#define seqan seqan
^
/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:221:9: note: in expansion of macro ‘seqan’
seqan::viewRecords(long_reads, long_read_bam, info.long_read_bai, rID_long, var_ref_pos_sub50, var_ref_pos_add50);
^
/scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘viewRecords’ is not a member of ‘seqan’
#define seqan seqan
^
/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:223:9: note: in expansion of macro ‘seqan’
seqan::viewRecords(long_reads, long_read_bam, info.long_read_bai, rID_long, var_ref_pos_end_sub50, var_ref_pos_end_add50);
^
/scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘viewRecords’ is not a member of ‘seqan’
#define seqan seqan
^
/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:379:17: note: in expansion of macro ‘seqan’
seqan::viewRecords(short_reads, short_read_bam, info.short_read_bai, rID_short, ref_region_start, e);
^
/scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘viewRecords’ is not a member of ‘seqan’
#define seqan seqan
^
/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:385:17: note: in expansion of macro ‘seqan’
seqan::viewRecords(tmp_short_reads, short_read_bam, info.short_read_bai, rID_short, s, ref_region_end);
^
/scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘viewRecords’ is not a member of ‘seqan’
#define seqan seqan
^
/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:392:17: note: in expansion of macro ‘seqan’
seqan::viewRecords(short_reads, short_read_bam, info.short_read_bai, rID_short, ref_region_start, ref_region_end);
^
/scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘ConvexGaps’ is not a member of ‘seqan’
#define seqan seqan
^
/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:460:28: note: in expansion of macro ‘seqan’
seqan::ConvexGaps());
^
make[3]: *** [CMakeFiles/sviper.dir/src/sviper.cpp.o] Error 1
make[2]: *** [CMakeFiles/sviper.dir/all] Error 2
make[1]: *** [CMakeFiles/sviper.dir/rule] Error 2
make: *** [sviper] Error 2

[Anzy-99]

Hi, I'm having the same installation problem as you. If you have solved the problem, can you tell me how to do it? Thanks!

[smehringer]

Hi @aserres and @Anzy-99,

I'm very sorry to get back to you so late but I was on maternity leave this year until a few weeks ago.

Let's trouble shoot.

First: When cloning SViper, did you use the git option --recurse-submodules?
If not or if you are not sure. Go to the SViper directory and type

git submodule update --init

Remove everything in the build directory and try using cmake and make again.

[shwetaramdas]

I'm having the same problem on my system. I didn't use 'git clone' to get SViper on my machine, but downloaded the zip from Github, and unzipped, and then followed the instructions (mkdir build --> cmake ../ --> make sviper)

I added the include path from my seqan installation to CMAKE_PREFIX_PATH, but I get the same error as in the original post. Any leads on why this might be? Thank you!

[joelfnogueira]

For me works these way:
git clone https://github.com/smehringer/SViper.git
micromamba install -c bioconda seqan
micromamba install -c conda-forge cxx-compiler
micromamba install -c anaconda cmake
cd SViper
git submodule update --init
mkdir build
cd build
cmake ..
make sviper