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I am new to linux and c++. I am trying to run veins gym on Ubuntu-18.04. When I run snakemake -jall (see the link) I receive an error:

make: Entering directory '/home/rost/serpentine-env/src'
Creating executable: out/gcc-debug//experiment_dbg
/usr/bin/ld: cannot find -lprotobuf
collect2: error: ld returned 1 exit status
Makefile:96: recipe for target 'out/gcc-debug//experiment_dbg' failed
make: *** [out/gcc-debug//experiment_dbg] Error 1
make: Leaving directory '/home/rost/serpentine-env/src'
[Thu Dec 30 12:34:46 2021]
Error in rule build:
    jobid: 1
    output: src/experiment_dbg
    shell:
        make -j8 -C src MODE=debug
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/rost/serpentine-env/.snakemake/log/2021-12-30T123446.742985.snakemake.log

To obtain a little more information, I run (source)

ld -lprotobuf --verbose

and I get

attempt to open //usr/local/lib/x86_64-linux-gnu/libprotobuf.so failed
attempt to open //usr/local/lib/x86_64-linux-gnu/libprotobuf.a failed
attempt to open //lib/x86_64-linux-gnu/libprotobuf.so failed
attempt to open //lib/x86_64-linux-gnu/libprotobuf.a failed
attempt to open //usr/lib/x86_64-linux-gnu/libprotobuf.so failed
attempt to open //usr/lib/x86_64-linux-gnu/libprotobuf.a failed
attempt to open //usr/lib/x86_64-linux-gnu64/libprotobuf.so failed
attempt to open //usr/lib/x86_64-linux-gnu64/libprotobuf.a failed
attempt to open //usr/local/lib64/libprotobuf.so failed
attempt to open //usr/local/lib64/libprotobuf.a failed
attempt to open //lib64/libprotobuf.so failed
attempt to open //lib64/libprotobuf.a failed
attempt to open //usr/lib64/libprotobuf.so failed
attempt to open //usr/lib64/libprotobuf.a failed
attempt to open //usr/local/lib/libprotobuf.so failed
attempt to open //usr/local/lib/libprotobuf.a failed
attempt to open //lib/libprotobuf.so failed
attempt to open //lib/libprotobuf.a failed
attempt to open //usr/lib/libprotobuf.so failed
attempt to open //usr/lib/libprotobuf.a failed
attempt to open //usr/x86_64-linux-gnu/lib64/libprotobuf.so failed
attempt to open //usr/x86_64-linux-gnu/lib64/libprotobuf.a failed
attempt to open //usr/x86_64-linux-gnu/lib/libprotobuf.so failed
attempt to open //usr/x86_64-linux-gnu/lib/libprotobuf.a failed
ld: cannot find -lprotobuf

I guess, I would have to make symlink manually, but I do not find any .so files in the archives from protobuf. Or maybe my interpretation is wrong. If some information is missing - I will provide.

Thank you!

UPDATE:
after runningsudo apt install libprotobuf-dev, command snakemake -jall produces

make: Entering directory '/home/rost/serpentine-env/src'
Creating executable: out/gcc-debug//experiment_dbg
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Request::_InternalParse(char const*, google::protobuf::internal::ParseContext*)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:563: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:571: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:579: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:593: undefined reference to `google::protobuf::internal::UnknownFieldParse(unsigned long, google::protobuf::UnknownFieldSet*, char const*, google::protobuf::internal::ParseContext*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Request::_InternalSerialize(unsigned char*, google::protobuf::io::EpsCopyOutputStream*) const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:644: undefined reference to `google::protobuf::internal::WireFormat::InternalSerializeUnknownFieldsToArray(google::protobuf::UnknownFieldSet const&, unsigned char*, google::protobuf::io::EpsCopyOutputStream*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Request::ByteSizeLong() const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:690: undefined reference to `google::protobuf::Message::MaybeComputeUnknownFieldsSize(unsigned long, google::protobuf::internal::CachedSize*) const'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Request::GetMetadata() const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:757: undefined reference to `google::protobuf::internal::AssignDescriptors(google::protobuf::internal::DescriptorTable const* (*)(), std::once_flag*, google::protobuf::Metadata const&)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Reply::_InternalParse(char const*, google::protobuf::internal::ParseContext*)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:946: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:954: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:962: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:976: undefined reference to `google::protobuf::internal::UnknownFieldParse(unsigned long, google::protobuf::UnknownFieldSet*, char const*, google::protobuf::internal::ParseContext*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Reply::_InternalSerialize(unsigned char*, google::protobuf::io::EpsCopyOutputStream*) const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1027: undefined reference to `google::protobuf::internal::WireFormat::InternalSerializeUnknownFieldsToArray(google::protobuf::UnknownFieldSet const&, unsigned char*, google::protobuf::io::EpsCopyOutputStream*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Reply::ByteSizeLong() const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1073: undefined reference to `google::protobuf::Message::MaybeComputeUnknownFieldsSize(unsigned long, google::protobuf::internal::CachedSize*) const'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Reply::GetMetadata() const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1140: undefined reference to `google::protobuf::internal::AssignDescriptors(google::protobuf::internal::DescriptorTable const* (*)(), std::once_flag*, google::protobuf::Metadata const&)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Init::Init(veinsgym::proto::Init const&)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1166: undefined reference to `google::protobuf::internal::ArenaStringPtr::Set(google::protobuf::internal::ArenaStringPtr::EmptyDefault, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, google::protobuf::Arena*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1174: undefined reference to `google::protobuf::internal::ArenaStringPtr::Set(google::protobuf::internal::ArenaStringPtr::EmptyDefault, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, google::protobuf::Arena*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1182: undefined reference to `google::protobuf::internal::ArenaStringPtr::Set(google::protobuf::internal::ArenaStringPtr::EmptyDefault, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, google::protobuf::Arena*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Init::Clear()':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1233: undefined reference to `google::protobuf::internal::ArenaStringPtr::ClearToEmpty()'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1234: undefined reference to `google::protobuf::internal::ArenaStringPtr::ClearToEmpty()'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1235: undefined reference to `google::protobuf::internal::ArenaStringPtr::ClearToEmpty()'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Init::_InternalParse(char const*, google::protobuf::internal::ParseContext*)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1249: undefined reference to `google::protobuf::internal::InlineGreedyStringParser(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, char const*, google::protobuf::internal::ParseContext*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1259: undefined reference to `google::protobuf::internal::InlineGreedyStringParser(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, char const*, google::protobuf::internal::ParseContext*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1269: undefined reference to `google::protobuf::internal::InlineGreedyStringParser(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, char const*, google::protobuf::internal::ParseContext*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1284: undefined reference to `google::protobuf::internal::UnknownFieldParse(unsigned long, google::protobuf::UnknownFieldSet*, char const*, google::protobuf::internal::ParseContext*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Init::_InternalSerialize(unsigned char*, google::protobuf::io::EpsCopyOutputStream*) const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1335: undefined reference to `google::protobuf::internal::WireFormat::InternalSerializeUnknownFieldsToArray(google::protobuf::UnknownFieldSet const&, unsigned char*, google::protobuf::io::EpsCopyOutputStream*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Init::ByteSizeLong() const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1371: undefined reference to `google::protobuf::Message::MaybeComputeUnknownFieldsSize(unsigned long, google::protobuf::internal::CachedSize*) const'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Init::MergeFrom(veinsgym::proto::Init const&)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.h:2983: undefined reference to `google::protobuf::internal::ArenaStringPtr::Set(google::protobuf::internal::ArenaStringPtr::EmptyDefault, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, google::protobuf::Arena*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.h:3034: undefined reference to `google::protobuf::internal::ArenaStringPtr::Set(google::protobuf::internal::ArenaStringPtr::EmptyDefault, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, google::protobuf::Arena*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.h:3085: undefined reference to `google::protobuf::internal::ArenaStringPtr::Set(google::protobuf::internal::ArenaStringPtr::EmptyDefault, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, google::protobuf::Arena*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Init::GetMetadata() const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1441: undefined reference to `google::protobuf::internal::AssignDescriptors(google::protobuf::internal::DescriptorTable const* (*)(), std::once_flag*, google::protobuf::Metadata const&)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Shutdown::Shutdown(veinsgym::proto::Shutdown const&)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1456: undefined reference to `google::protobuf::internal::ZeroFieldsBase::~ZeroFieldsBase()'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Shutdown::GetMetadata() const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1480: undefined reference to `google::protobuf::internal::AssignDescriptors(google::protobuf::internal::DescriptorTable const* (*)(), std::once_flag*, google::protobuf::Metadata const&)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Step::_InternalParse(char const*, google::protobuf::internal::ParseContext*)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1580: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1588: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1602: undefined reference to `google::protobuf::internal::UnknownFieldParse(unsigned long, google::protobuf::UnknownFieldSet*, char const*, google::protobuf::internal::ParseContext*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Step::_InternalSerialize(unsigned char*, google::protobuf::io::EpsCopyOutputStream*) const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1639: undefined reference to `google::protobuf::internal::WireFormat::InternalSerializeUnknownFieldsToArray(google::protobuf::UnknownFieldSet const&, unsigned char*, google::protobuf::io::EpsCopyOutputStream*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Step::ByteSizeLong() const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1668: undefined reference to `google::protobuf::Message::MaybeComputeUnknownFieldsSize(unsigned long, google::protobuf::internal::CachedSize*) const'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Step::GetMetadata() const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1724: undefined reference to `google::protobuf::internal::AssignDescriptors(google::protobuf::internal::DescriptorTable const* (*)(), std::once_flag*, google::protobuf::Metadata const&)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Space::_InternalParse(char const*, google::protobuf::internal::ParseContext*)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:1992: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2000: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2008: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2016: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2024: undefined reference to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)'
out/gcc-debug//protobuf/veinsgym.pb.o:/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2032: more undefined references to `google::protobuf::internal::ParseContext::ParseMessage(google::protobuf::MessageLite*, char const*)' follow
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Space::_InternalParse(char const*, google::protobuf::internal::ParseContext*)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2046: undefined reference to `google::protobuf::internal::UnknownFieldParse(unsigned long, google::protobuf::UnknownFieldSet*, char const*, google::protobuf::internal::ParseContext*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Space::_InternalSerialize(unsigned char*, google::protobuf::io::EpsCopyOutputStream*) const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2115: undefined reference to `google::protobuf::internal::WireFormat::InternalSerializeUnknownFieldsToArray(google::protobuf::UnknownFieldSet const&, unsigned char*, google::protobuf::io::EpsCopyOutputStream*)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Space::ByteSizeLong() const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2177: undefined reference to `google::protobuf::Message::MaybeComputeUnknownFieldsSize(unsigned long, google::protobuf::internal::CachedSize*) const'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Space::GetMetadata() const':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2252: undefined reference to `google::protobuf::internal::AssignDescriptors(google::protobuf::internal::DescriptorTable const* (*)(), std::once_flag*, google::protobuf::Metadata const&)'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Box::Box(google::protobuf::Arena*, bool)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2264: undefined reference to `google::protobuf::RepeatedField<double>::RepeatedField(google::protobuf::Arena*)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2264: undefined reference to `google::protobuf::RepeatedField<double>::~RepeatedField()'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Box::Box(veinsgym::proto::Box const&)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2273: undefined reference to `google::protobuf::RepeatedField<double>::RepeatedField(google::protobuf::RepeatedField<double> const&)'
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2273: undefined reference to `google::protobuf::RepeatedField<double>::~RepeatedField()'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Box::~Box()':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2281: undefined reference to `google::protobuf::RepeatedField<double>::~RepeatedField()'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Box::Clear()':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2308: undefined reference to `google::protobuf::RepeatedField<double>::Clear()'
out/gcc-debug//protobuf/veinsgym.pb.o: In function `veinsgym::proto::Box::_InternalParse(char const*, google::protobuf::internal::ParseContext*)':
/home/rost/serpentine-env/src/protobuf/veinsgym.pb.cc:2321: undefined reference to `google::protobuf::internal::PackedDoubleParser(void*, char const*, google::protobuf::internal::ParseContext*)'
...
/home/rost/serpentine-env/src/./protobuf/veinsgym.pb.h:780: undefined reference to `google::protobuf::internal::ZeroFieldsBase::InternalSwap(google::protobuf::internal::ZeroFieldsBase*)'
out/gcc-debug//serpentine/GymSplitter.o: In function `veinsgym::proto::Shutdown::CopyFrom(veinsgym::proto::Shutdown const&)':
/home/rost/serpentine-env/src/./protobuf/veinsgym.pb.h:835: undefined reference to `google::protobuf::internal::ZeroFieldsBase::CopyImpl(google::protobuf::Message*, google::protobuf::Message const&)'
out/gcc-debug//serpentine/GymSplitter.o: In function `veinsgym::proto::Box::set_values(int, double)':
/home/rost/serpentine-env/src/./protobuf/veinsgym.pb.h:3778: undefined reference to `google::protobuf::RepeatedField<double>::Set(int, double const&)'
out/gcc-debug//serpentine/GymSplitter.o: In function `void google::protobuf::RepeatedField<double>::Add<double const*>(double const*, double const*)':
/usr/local/include/google/protobuf/repeated_field.h:705: undefined reference to `google::protobuf::RepeatedField<double>::size() const'
/usr/local/include/google/protobuf/repeated_field.h:712: undefined reference to `google::protobuf::RepeatedField<double>::elements() const'
/usr/local/include/google/protobuf/repeated_field.h:712: undefined reference to `google::protobuf::RepeatedField<double>::size() const'
/usr/local/include/google/protobuf/repeated_field.h:713: undefined reference to `google::protobuf::RepeatedField<double>::size() const'
out/gcc-debug//serpentine/GymSplitter.o: In function `google::protobuf::RepeatedField<double>::FastAdderImpl<0, true>::FastAdderImpl(google::protobuf::RepeatedField<double>*)':
/usr/local/include/google/protobuf/repeated_field.h:448: undefined reference to `google::protobuf::RepeatedField<double>::unsafe_elements() const'
out/gcc-debug//serpentine/GymSplitter.o: In function `google::protobuf::RepeatedField<double>::FastAdderImpl<0, true>::Add(double)':
/usr/local/include/google/protobuf/repeated_field.h:457: undefined reference to `google::protobuf::RepeatedField<double>::unsafe_elements() const'
collect2: error: ld returned 1 exit status
Makefile:96: recipe for target 'out/gcc-debug//experiment_dbg' failed
make: *** [out/gcc-debug//experiment_dbg] Error 1
make: Leaving directory '/home/rost/serpentine-env/src'
Python
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  • How have you installed protobuf? – Alan Birtles Dec 30 '21 at 12:28
  • @AlanBirtles yes, I have also added it to PATH – Python Dec 30 '21 at 12:28
  • **how** have you installed protobuf? – Alan Birtles Dec 30 '21 at 12:30
  • @AlanBirtles from https://github.com/protocolbuffers/protobuf/releases I have downloaded `protoc-3.19.1-linux-x86_64.zip`. I have unpacked the archive and from the `bin` folder I have copied `protoc` to `/usr/bin` so it is included in PATH. Also, I have downloaded `Source code (tar.gz)` and from `src` directory copied `google` folder into `\usr\local\include` – Python Dec 30 '21 at 12:39
  • Sounds like you never built Protobuf (preferably with CMake) but rather you just copied source files to `/usr/local/include`. Once you unpack the tar-ball, run "the usual" CMake build (`mkdir build && cd build && cmake .. & sudo make install`) to install the libs/binaries to `/usr/local/` – mdf Dec 30 '21 at 14:05
  • 1
    `sudo apt install libprotobuf-dev` – 273K Dec 30 '21 at 14:54
  • @273K after installing `libprotobuf-dev`, error changed a little (see update) – Python Dec 30 '21 at 15:08
  • @mdf you are probably right, I am working on this now... – Python Dec 30 '21 at 15:09
  • Remove all garbage that you copied manually before installing libprotobuf-dev. – 273K Dec 30 '21 at 15:13
  • @273K I have removed `google` folder from `/usr/local/include` and also `protoc` file from `/usr/bin`. Then I restarted the shell and ran `snakemake -jall` but the error stays the same :( – Python Dec 30 '21 at 15:39

0 Answers0