Error while installing Minia on Linux
I have been trying to install the short read assembler Minia on my linux system but whenever I am giving the "make" command this error is coming up.
[ 71%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o
In file included from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:35,
from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:33,
from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/Storage.tpp:509,
from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:666,
from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:43,
from /home/minia/thirdparty/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20,
from /home/minia/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5
/home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp: In copy constructor
'gatb::core::tools::collections::impl::IteratorGzFile<Item>::IteratorGzFile(const
gatb::core::tools::collections::impl::IteratorGzFile<Item>&)':
/home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:242:9: error: there are no
arguments to 'gzbuffer' that depend on a template parameter, so a declaration of 'gzbuffer' must be available [-
fpermissive]
242 | gzbuffer(_gzfile,2*1024*1024);
| ^~~~~~~~
/home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:242:9: note: (if you use '-
fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp: In constructor
'gatb::core::tools::collections::impl::IteratorGzFile<Item>::IteratorGzFile(const string&, size_t)':
/home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:252:9: error: there are no
arguments to 'gzbuffer' that depend on a template parameter, so a declaration of 'gzbuffer' must be available [-
fpermissive]
252 | gzbuffer(_gzfile,2*1024*1024);
| ^~~~~~~~
/home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp: In member function
'gatb::core::tools::collections::impl::IteratorGzFile<Item>&
gatb::core::tools::collections::impl::IteratorGzFile<Item>::operator=(const
gatb::core::tools::collections::impl::IteratorGzFile<Item>&)':
/home/minia/thirdparty/gatb-core/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:278:13: error: there are
no arguments to 'gzbuffer' that depend on a template parameter, so a declaration of 'gzbuffer' must be available [-
fpermissive]
278 | gzbuffer(_gzfile,2*1024*1024);
| ^~~~~~~~
make[2]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-
static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o] Error 1
make[1]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/all] Error 2
make: *** [all] Error 2
I am following the installation from their manual. Please can anyone help me? Thanks
• 1,665 views
•
link
0 answers
No answers yet.
Log in to answer this question.
Miniconda can be used for minia installation.
Or even better, use the corresponding
biocontainersdocker container and use it with docker/singularity@MSRS thank you so much.