Comments (10)
dancooke
commented on August 30, 2024
This is weird. I can replicate this in a CentOS 7 Docker container. It looks like the wrong libstdc++ ABI is getting selected for some reason. I'll look into it!
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ink1
commented on August 30, 2024
Daniel, thank you for looking into this.
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dancooke
commented on August 30, 2024
The problem is that the GCC you're using wasn't configured to use a C++11 compatible ABI by default. Probably because you obtained GCC from RPM, which for reasons I don't quite understand, wasn't configured with the new C++ ABI (see my Stack Overflow question).
Unfortunately, the only way I've managed to resolve this is to install GCC 7 manually from source. You will also need to reinstall Boost and make sure it's compiled with the new GCC install. I've put together a Dockerfile (see below) which installs octopus on a fresh Centos 7 image. You should be able use this as a guide. In particular, it shows how to manually install GCC 7 with the correct ABI, and also how to install Boost correctly. Don't forget to remove the GCC 7 (including the packaged libstdc++) and Boost libraries you previously installed. Let me know if you need any help.
You will need the latest develop branch version if you want to use the install.py helper script as shown here; I've only just added the c_compiler option to this. It turns out specifying the C compiler, in addition to the C++ compiler, is important on some systems (as you were already doing, but with cmake directly).
# Dockerfile to install octopus, including any dependencies, on a fresh Centos 7 image.
FROM centos:latest
# Install all packaged dependencies
RUN yum -y update
RUN yum -y install \
which \
yum-utils \
gcc \
gcc-c++ \
make \
wget \
git \
autoconf \
openssl \
bzip2.x86_64 \
bzip2-devel.x86_64 \
xz-devel.x86_64 \
zlib-devel.x86_64 \
libcurl-devel.x86_64
# Install GCC 7
WORKDIR /tmp
RUN wget ftp://ftp.mirrorservice.org/sites/sourceware.org/pub/gcc/releases/gcc-7.2.0/gcc-7.2.0.tar.gz
RUN tar -xvzf gcc-7.2.0.tar.gz
WORKDIR /tmp/gcc-7.2.0
RUN contrib/download_prerequisites
WORKDIR /tmp
RUN mkdir mkdir gcc-7.2.0-build
WORKDIR /tmp/gcc-7.2.0-build
RUN ../gcc-7.2.0/configure \
--enable-bootstrap \
--enable-languages=c,c++,fortran,lto \
--with-bugurl=http://bugzilla.redhat.com/bugzilla \
--enable-shared \
--enable-threads=posix \
--enable-checking=release \
--disable-multilib \
--with-system-zlib \
--enable-__cxa_atexit \
--disable-libunwind-exceptions \
--enable-gnu-unique-object \
--enable-linker-build-id \
--with-gcc-major-version-only \
--enable-plugin \
--with-linker-hash-style=gnu \
--enable-initfini-array \
--enable-libmpx \
--enable-gnu-indirect-function \
--with-tune=generic \
--build=x86_64-redhat-linux
RUN make -j4
RUN make install
ENV LD_LIBRARY_PATH /usr/local/lib:/usr/local/lib64
# Install Python3
WORKDIR /tmp
RUN yum-builddep -y python
RUN curl -O https://www.python.org/ftp/python/3.5.0/Python-3.5.0.tgz
RUN tar xf Python-3.5.0.tgz
WORKDIR /tmp/Python-3.5.0
RUN ./configure
RUN make -j2
RUN make install
# Install CMake
WORKDIR /tmp
RUN wget https://cmake.org/files/v3.9/cmake-3.9.6.tar.gz
RUN tar -xzvf cmake-3.9.6.tar.gz
WORKDIR /tmp/cmake-3.9.6
RUN ./bootstrap --prefix=/usr/local
RUN make -j2
RUN make install
# Install Boost
WORKDIR /tmp
RUN wget -O boost_1_65_1.tar.gz http://sourceforge.net/projects/boost/files/boost/1.65.1/boost_1_65_1.tar.gz/download
RUN tar xzvf boost_1_65_1.tar.gz
WORKDIR /tmp/boost_1_65_1
RUN ./bootstrap.sh --prefix=/usr/local --without-libraries=python,mpi
RUN ./b2 cxxflags="-std=c++11"
RUN ./b2 install
# Install htslib
WORKDIR /tmp
RUN git clone https://github.com/samtools/htslib.git
WORKDIR /tmp/htslib
RUN autoheader
RUN autoconf
RUN ./configure
RUN make -j4
RUN make install
# Install Octopus
WORKDIR /tmp
RUN git clone https://github.com/luntergroup/octopus.git
WORKDIR /tmp/octopus
RUN ./install.py --root --threads=2 --cxx_compiler=/usr/local/bin/g++ --c_compiler=/usr/local/bin/gcc
WORKDIR /home
RUN octopus --helpfrom octopus.
ink1
commented on August 30, 2024
Thank you for providing the Dockerfile. This is helpful. I did build gcc 7.2 from source myself but selected compatible ABI because I wanted to avoid rebuilding the full software stack required for Octopus. Selecting incompatible ABI could be messy and error prone path so wanted to avoid this. Docker is one way to tackle this but we don't support it on our HPC cluster. Do you think Singularity can be used to wrap this up?
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dancooke
commented on August 30, 2024
The only thing that would need rebuilding is Boost. You could even have a separate Boost installation if you don't want to overwrite your existing one. You may need to set the boost root path for cmake (either with DBOOST_ROOT with cmake directly, or --boost with the python installer) if you do so. I don't really understand the rational of having GCC 7 configured with a non-C++11 ABI - it severely limits the functionality of the compiler. The Ubuntu maintained GCC package doesn't do this.
I wouldn't recommend using Docker for production runs anyway as it will likely run much slower the a native install - I just use it for debugging. I'm afraid I don't have any experience with Singularity.
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dancooke
commented on August 30, 2024
I'm going to close this as there isn't really anything I can do - essentially the issue is an unmet requirement. Perhaps I'll look at providing pre-compiled binaries in future releases.
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lachlansimpson
commented on August 30, 2024
Hmmm. I also seem to have run into this problem. As noted elsewhere, I used devtoolset-7 install rather than install gcc 7 myself.
./scripts/install.py --boost /config/binaries/boost/1.68.0/
[ 35%] Building CXX object src/CMakeFiles/octopus.dir/core/callers/caller_builder.cpp.o
[ 36%] Building CXX object src/CMakeFiles/octopus.dir/core/callers/caller_factory.cpp.o
/config/source/octopus/src/utils/memory_footprint.cpp: In function ‘boost::optional<octopus::MemoryFootprint> octopus::parse_footprint(std::string)’:
/config/source/octopus/src/utils/memory_footprint.cpp:189:64: error: no matching function for call to ‘std::basic_string<char>::erase(__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >&, std::basic_string<char>::const_iterator)’
footprint_str.erase(last_digit_itr, cend(footprint_str));
^
In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/string:52:0,
from /config/source/octopus/src/utils/memory_footprint.hpp:8,
from /config/source/octopus/src/utils/memory_footprint.cpp:4:
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>& std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::size_type, std::basic_string<_CharT, _Traits, _Alloc>::
size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]
erase(size_type __pos = 0, size_type __n = npos)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: no known conversion for argument 1 from ‘__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >’ to ‘std::basic_string<char>::size_type {aka long unsigned int}’
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator) [with _CharT = char; _Traits = std::
char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __position)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate expects 1 argument, 2 provided
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator, std::basic_string<_CharT, _Traits, _
Alloc>::iterator) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __first, iterator __last);
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: no known conversion for argument 1 from ‘__gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >’ to ‘std::basic_string<char>::iterator {aka __gnu_cxx::__normal_iterator<char*, std::basic_st
ring<char> >}’
make[2]: *** [src/CMakeFiles/octopus.dir/build.make:752: src/CMakeFiles/octopus.dir/utils/memory_footprint.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/config/source/octopus/src/utils/genotype_reader.cpp: In function ‘boost::optional<octopus::BasicAllele<octopus::ContigRegion> > octopus::{anonymous}::make_allele(const octopus::VcfRecord&, octopus::VcfRecord::NucleotideSequence, int)’:
/config/source/octopus/src/utils/genotype_reader.cpp:127:75: error: no matching function for call to ‘std::basic_string<char>::erase(std::basic_string<char>::const_iterator, __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >&)’
allele_sequence.erase(std::cbegin(allele_sequence), first_base_itr);
^
In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/string:52:0,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/stdexcept:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/array:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/tuple:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/functional:54,
from /config/source/octopus/src/utils/genotype_reader.hpp:7,
from /config/source/octopus/src/utils/genotype_reader.cpp:4:
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>& std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::size_type, std::basic_string<_CharT, _Traits, _Alloc>::
size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]
erase(size_type __pos = 0, size_type __n = npos)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: no known conversion for argument 1 from ‘std::basic_string<char>::const_iterator {aka __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >}’ to ‘std::basic_string<char>::size_type {aka lo
ng unsigned int}’
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator) [with _CharT = char; _Traits = std::
char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __position)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate expects 1 argument, 2 provided
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator, std::basic_string<_CharT, _Traits, _
Alloc>::iterator) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __first, iterator __last);
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: no known conversion for argument 1 from ‘std::basic_string<char>::const_iterator {aka __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >}’ to ‘std::basic_string<char>::iterator {aka __g
nu_cxx::__normal_iterator<char*, std::basic_string<char> >}’
/config/source/octopus/src/utils/genotype_reader.cpp:132:69: error: no matching function for call to ‘std::basic_string<char>::erase(std::basic_string<char>::const_iterator, __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >&)’
allele_sequence.erase(std::cbegin(allele_sequence), p.second);
^
In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/string:52:0,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/stdexcept:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/array:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/tuple:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/functional:54,
from /config/source/octopus/src/utils/genotype_reader.hpp:7,
from /config/source/octopus/src/utils/genotype_reader.cpp:4:
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>& std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::size_type, std::basic_string<_CharT, _Traits, _Alloc>::
size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]
erase(size_type __pos = 0, size_type __n = npos)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: no known conversion for argument 1 from ‘std::basic_string<char>::const_iterator {aka __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >}’ to ‘std::basic_string<char>::size_type {aka lo
ng unsigned int}’
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator) [with _CharT = char; _Traits = std::
char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __position)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate expects 1 argument, 2 provided
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator, std::basic_string<_CharT, _Traits, _
Alloc>::iterator) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __first, iterator __last);
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: no known conversion for argument 1 from ‘std::basic_string<char>::const_iterator {aka __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >}’ to ‘std::basic_string<char>::iterator {aka __g
nu_cxx::__normal_iterator<char*, std::basic_string<char> >}’
/config/source/octopus/src/utils/genotype_reader.cpp: In function ‘std::pair<std::vector<octopus::BasicAllele<octopus::GenomicRegion> >, bool> octopus::get_called_alleles(const octopus::VcfRecord&, const SampleName&, bool)’:
/config/source/octopus/src/utils/genotype_reader.cpp:217:82: error: no matching function for call to ‘std::basic_string<char>::erase(std::basic_string<char>::const_iterator, __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >)’
ref.erase(std::cbegin(ref), std::next(std::cbegin(ref), *max_ref_pad));
^
In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/string:52:0,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/stdexcept:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/array:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/tuple:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/functional:54,
from /config/source/octopus/src/utils/genotype_reader.hpp:7,
from /config/source/octopus/src/utils/genotype_reader.cpp:4:
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>& std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::size_type, std::basic_string<_CharT, _Traits, _Alloc>::
size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]
erase(size_type __pos = 0, size_type __n = npos)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: no known conversion for argument 1 from ‘std::basic_string<char>::const_iterator {aka __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >}’ to ‘std::basic_string<char>::size_type {aka lo
ng unsigned int}’
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator) [with _CharT = char; _Traits = std::
char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __position)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate expects 1 argument, 2 provided
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator, std::basic_string<_CharT, _Traits, _
Alloc>::iterator) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __first, iterator __last);
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: no known conversion for argument 1 from ‘std::basic_string<char>::const_iterator {aka __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >}’ to ‘std::basic_string<char>::iterator {aka __g
nu_cxx::__normal_iterator<char*, std::basic_string<char> >}’
/config/source/octopus/src/utils/genotype_reader.cpp:227:59: error: no matching function for call to ‘std::basic_string<char>::erase(std::basic_string<char>::const_iterator, __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >&)’
allele.erase(std::cbegin(allele), p.second);
^
In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/string:52:0,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/stdexcept:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/array:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/tuple:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/functional:54,
from /config/source/octopus/src/utils/genotype_reader.hpp:7,
from /config/source/octopus/src/utils/genotype_reader.cpp:4:
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>& std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::size_type, std::basic_string<_CharT, _Traits, _Alloc>::
size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]
erase(size_type __pos = 0, size_type __n = npos)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: no known conversion for argument 1 from ‘std::basic_string<char>::const_iterator {aka __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >}’ to ‘std::basic_string<char>::size_type {aka lo
ng unsigned int}’
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator) [with _CharT = char; _Traits = std::
char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __position)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate expects 1 argument, 2 provided
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator, std::basic_string<_CharT, _Traits, _
Alloc>::iterator) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __first, iterator __last);
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: no known conversion for argument 1 from ‘std::basic_string<char>::const_iterator {aka __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >}’ to ‘std::basic_string<char>::iterator {aka __g
nu_cxx::__normal_iterator<char*, std::basic_string<char> >}’
/config/source/octopus/src/utils/genotype_reader.cpp: In instantiation of ‘octopus::get_called_alleles(const octopus::VcfRecord&, const SampleName&, bool)::<lambda(auto:163&)> [with auto:163 = std::basic_string<char>]’:
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_algo.h:3884:5: required from ‘_Funct std::for_each(_IIter, _IIter, _Funct) [with _IIter = __gnu_cxx::__normal_iterator<std::basic_string<char>*, std::vector<std::basic_string<char> > >; _Funct = octopus::get_called_alleles(cons
t octopus::VcfRecord&, const SampleName&, bool)::<lambda(auto:163&)>]’
/config/source/octopus/src/utils/genotype_reader.cpp:211:10: required from here
/config/source/octopus/src/utils/genotype_reader.cpp:199:17: error: no matching function for call to ‘std::basic_string<char>::erase(std::basic_string<char>::const_iterator, __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >)’
allele.erase(std::cbegin(allele), std::next(std::cbegin(allele), pad_size));
^~~~~~
In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/string:52:0,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/stdexcept:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/array:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/tuple:39,
from /opt/rh/devtoolset-7/root/usr/include/c++/7/functional:54,
from /config/source/octopus/src/utils/genotype_reader.hpp:7,
from /config/source/octopus/src/utils/genotype_reader.cpp:4:
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>& std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::size_type, std::basic_string<_CharT, _Traits, _Alloc>::
size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]
erase(size_type __pos = 0, size_type __n = npos)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4613:7: note: no known conversion for argument 1 from ‘std::basic_string<char>::const_iterator {aka __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >}’ to ‘std::basic_string<char>::size_type {aka lo
ng unsigned int}’
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator) [with _CharT = char; _Traits = std::
char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __position)
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4629:7: note: candidate expects 1 argument, 2 provided
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: candidate: std::basic_string<_CharT, _Traits, _Alloc>::iterator std::basic_string<_CharT, _Traits, _Alloc>::erase(std::basic_string<_CharT, _Traits, _Alloc>::iterator, std::basic_string<_CharT, _Traits, _
Alloc>::iterator) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::basic_string<_CharT, _Traits, _Alloc>::iterator = __gnu_cxx::__normal_iterator<char*, std::basic_string<char> >; typename _Alloc::rebind<_CharT>::other::pointer = char*]
erase(iterator __first, iterator __last);
^~~~~
/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:4649:7: note: no known conversion for argument 1 from ‘std::basic_string<char>::const_iterator {aka __gnu_cxx::__normal_iterator<const char*, std::basic_string<char> >}’ to ‘std::basic_string<char>::iterator {aka __g
nu_cxx::__normal_iterator<char*, std::basic_string<char> >}’
make[2]: *** [src/CMakeFiles/octopus.dir/build.make:778: src/CMakeFiles/octopus.dir/utils/genotype_reader.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:281: src/CMakeFiles/octopus.dir/all] Error 2
make: *** [Makefile:130: all] Error 2
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dancooke
commented on August 30, 2024
@datakid As noted in my post above, the GCC7 yum package was built using the pre-C++11 ABI, which basically makes it incompatible with the C++11 standard library without some code hacks. This seems like a very strange decision to me; it's not like this on the Ubunutu package. So your choices are to either build GCC7 (or even 8 now) yourself (also in my post above), or you could just use the Bioconda package.
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lachlansimpson
commented on August 30, 2024
Sorry, I see the same complaint elsewhere. Cheers
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lachlansimpson
commented on August 30, 2024
For those that come after me, here's the relevant answer on SO.
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Related Issues (20)
- can not download the forest files HOT 1
- Remove depreciated inheritance of std::unary_function
- Call in high heterozygotes
- VCF file is empty
- info on UL nanpore reads HOT 2
- Forest file is still not available for donwloading "std::bad_alloc Error" HOT 9
- Population-level variant calling using accessions with complex ploidy level
- Will octopus add a mode using paired information to compose a linked debruijn graph?
- Can octopus add a feature to add supported read query names of the variants in the INFO field of the output VCF file? HOT 1
- Position of maternal or paternal haplotypes in Octopus after performing TRIO analyses HOT 1
- Models for NovaseqX?
- Encountered an exception during calling 'std::bad_alloc' HOT 2
- training data & regions of the genome used for somatic random forest model
- Build failures on `gcc-13`: `option_collation.cpp:1298: error: redundant move in initialization`
- Build fails, is there a singularity? HOT 1
- ERROR in reading reference index. HOT 2
- Starting Call Set Refinement (CSR) filtering provokes RAM overload HOT 2
- Use with Nanopore long reads HOT 2
- After recompiling from source get error 'Phred: negative error [2024-07-15 12:55:12] <EROR> probability -0.000000' HOT 2
- Binaries compiled for AVX-512 cores do not process the whole genome. HOT 2
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