install failed

[xiaomiyang36]

Hi, I have met problem when I installed minimac4 . the command I used as follow:
/home/rw/guanglinHe/software/anaconda3/bin/cget install -f ./requirements.txt #-- Installing:/home/XiaominYang/biosoftware/Minimac4/cget/cget/pkg/statgen__libStatGen/install/lib/libStatGen.a
Successfully installed statgen/libStatGen
mkdir build && cd build
cmake -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake ..
make

the problem as follow:
Scanning dependencies of target minimac4
[ 8%] Building CXX object CMakeFiles/minimac4.dir/src/Analysis.cpp.o
[ 16%] Building CXX object CMakeFiles/minimac4.dir/src/AnalysisChunks.cpp.o
[ 25%] Building CXX object CMakeFiles/minimac4.dir/src/DosageData.cpp.o
[ 33%] Building CXX object CMakeFiles/minimac4.dir/src/HaplotypeSet.cpp.o
[ 41%] Building CXX object CMakeFiles/minimac4.dir/src/Imputation.cpp.o
[ 50%] Building CXX object CMakeFiles/minimac4.dir/src/ImputationStatistics.cpp.o
[ 58%] Building CXX object CMakeFiles/minimac4.dir/src/Main.cpp.o
[ 66%] Building CXX object CMakeFiles/minimac4.dir/src/MarkovModel.cpp.o
[ 75%] Building CXX object CMakeFiles/minimac4.dir/src/MarkovParameters.cpp.o
[ 83%] Building CXX object CMakeFiles/minimac4.dir/src/Unique.cpp.o
[ 91%] Building CXX object CMakeFiles/minimac4.dir/src/Estimation.cpp.o
[100%] Linking CXX executable minimac4
/usr/bin/ld: ../cget/lib/libStatGen.a(InputFile.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(Parameters.o): relocation R_X86_64_32S against symbol _ZTV13ParameterList' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(PhoneHome.o): relocation R_X86_64_32S against symbol _ZN9PhoneHome6ourURLB5cxx11E' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(StringBasics.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(StringMap.o): relocation R_X86_64_32S against symbol _ZTV9StringMap' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(UncompressedFileType.o): relocation R_X86_64_32S against symbol _ZTV20UncompressedFileType' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(VcfFile.o): relocation R_X86_64_32S against symbol _ZTV7VcfFile' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(VcfFileReader.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(VcfHeader.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(VcfRecord.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(VcfRecordFilter.o): relocation R_X86_64_32 against .bss' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(VcfRecordGenotype.o): relocation R_X86_64_32S against symbol _ZN17VcfRecordGenotype14ourStoreFieldsB5cxx11E' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(VcfRecordInfo.o): relocation R_X86_64_32S against symbol _ZTV13VcfRecordInfo' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(VcfSubsetSamples.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(VcfRecordDiscardRules.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(knetfile.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(BgzfFileType.o): relocation R_X86_64_32S against symbol _ZTV12BgzfFileType' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(BgzfFileTypeRecovery.o): relocation R_X86_64_32S against symbol _ZTV10FileReader' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(Error.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(FileType.o): relocation R_X86_64_32S against symbol _ZTV8FileType' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(GzipFileType.o): relocation R_X86_64_32S against symbol _ZTV12GzipFileType' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(GzipHeader.o): relocation R_X86_64_32S against symbol _ZN20UncompressedFileType6isOpenEv' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(StatGenStatus.o): relocation R_X86_64_32S against symbol _ZN13StatGenStatus16enumStatusStringE' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(StringArray.o): relocation R_X86_64_32S against symbol _ZTV11StringArray' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(Tabix.o): relocation R_X86_64_32S against symbol _ZTV5Tabix' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(VcfGenotypeField.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(VcfGenotypeFormat.o): relocation R_X86_64_32S against symbol _ZTV17VcfGenotypeFormat' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(VcfGenotypeSample.o): relocation R_X86_64_32S against symbol _ZTV17VcfGenotypeSample' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(bgzf.o): relocation R_X86_64_32S against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(ErrorHandler.o): relocation R_X86_64_32 against symbol _ZSt4cerr@@GLIBCXX_3.4' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: ../cget/lib/libStatGen.a(IndexBase.o): relocation R_X86_64_32S against symbol _ZTV9IndexBase' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ../cget/lib/libStatGen.a(Sort.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
CMakeFiles/minimac4.dir/build.make:356: recipe for target 'minimac4' failed
make[2]: *** [minimac4] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/minimac4.dir/all' failed
make[1]: *** [CMakeFiles/minimac4.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2

I will be appreciated if anyone can give me somea suggestions.

[jonathonl]

Try removing the cget directory in the base of the Minimac 4 source, running export CFLAGS="-fPIC", and then rerunning cget, cmake, and make.

[jonathonl]

Alternatively, you might be able to just run export CFLAGS="-no-pie" && make clean && make from the build directory.

[xiaomiyang36]

Try removing the cget directory in the base of the Minimac 4 source, running export CFLAGS="-fPIC", and then rerunning cget, cmake, and make.

I tried and failed to make , the error as follow:
[100%] Linking CXX executable minimac4
../cget/lib/libStatGen.a(StringBasics.o): In function String::appendFullFloat(float)': StringBasics.cpp:(.text+0x1082): undefined reference to std::__cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::basic_ostringstream()'
../cget/lib/libStatGen.a(VcfGenotypeSample.o): In function VcfGenotypeSample::updateGTString()': VcfGenotypeSample.cpp:(.text+0xaac): undefined reference to std::__cxx11::basic_stringstream<char, std::char_traits, std::allocator >::basic_stringstream()'
collect2: error: ld returned 1 exit status
CMakeFiles/minimac4.dir/build.make:356: recipe for target 'minimac4' failed
make[2]: *** [minimac4] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/minimac4.dir/all' failed
make[1]: *** [CMakeFiles/minimac4.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2

[jonathonl]

These link errors you are experiencing suggest that Minimac4 and libStatGen are being built with different compilers. You could try running export CFLAGS="-fPIC -D_GLIBCXX_USE_CXX11_ABI=0" && make.

If that doesn't work, please provide the output of uname -a; cat /etc/os-release; c++ --version; which c++ and attach the entire log output from cget, cmake, and make commands as separate files.

[xiaomiyang36]

These link errors you are experiencing suggest that Minimac4 and libStatGen are being built with different compilers. You could try running export CFLAGS="-fPIC -D_GLIBCXX_USE_CXX11_ABI=0" && make.

If that doesn't work, please provide the output of uname -a; cat /etc/os-release; c++ --version; which c++ and attach the entire log output from cget, cmake, and make commands as separate files.

I tried to run export CFLAGS="-fPIC -D_GLIBCXX_USE_CXX11_ABI=0" && make and the same problem occured. Those output logfile as follow
Thank you a billion!
output.zip

[jonathonl]

I'm guessing that libStatGen is being built with /usr/local/bin/c++ or /usr/local/bin/g++ and Minimac4 is being built with /usr/bin/c++. You might be able to solve this by reconfiguring Minimac4 from the build directory with:

cmake -DCMAKE_CXX_COMPILER=/usr/local/bin/c++ .. && make clean && make VERBOSE=1

Otherwise, I would just use the prebuilt binary at https://github.com/statgen/Minimac4/releases/download/v1.0.2/minimac4-1.0.2-Linux.sh. You can install the binary to a location of your choosing with bash minimac4-1.0.2-Linux.sh --prefix=/location/of/your/choosing

[xiaomiyang36]

prefix=/

This does work.
Than you very much!!!

[tragic-comedy]

Can I ask for some help? I ran into some trouble while installing Minimac4 and would greatly appreciate it. I tried the following steps:
"git clone https://github.com/statgen/Minimac4.git
cd Minimac4
bash install.sh"
but it failed:
bash install.sh
Installing Dependencies - Libstatgen ...
Generating MakeFiles ...
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
OMPP_LIBRARY
linked by target "minimac4" in directory /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master

CMake Error in CMakeLists.txt:
Imported target "savvy" includes non-existent path

"/home/hunau/mahj/anaconda3/envs/py3.11/include/htslib"

in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:

• The path was deleted, renamed, or moved to another location.

• An install or uninstall procedure did not complete successfully.

• The installation package was faulty and references files it does not
  provide.

-- Generating done
CMake Generate step failed. Build files cannot be regenerated correctly.
[ 14%] Building CXX object CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:4:0,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/streambuf: In constructor ‘shrinkwrap::stdio::filebuf::filebuf(shrinkwrap::stdio::filebuf::self_type&&)’:
/usr/include/c++/4.8.2/streambuf:802:7: error: ‘std::basic_streambuf<_CharT, _Traits>::basic_streambuf(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits]’ is private
basic_streambuf(const basic_streambuf& sb)
^
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4:0,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:27:20: error: within this context
fp(src.fp)
^
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:4:0,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/streambuf: In member function ‘shrinkwrap::stdio::filebuf::self_type& shrinkwrap::stdio::filebuf::operator=(shrinkwrap::stdio::filebuf::self_type&&)’:
/usr/include/c++/4.8.2/streambuf:810:7: error: ‘std::basic_streambuf<_CharT, _Traits>& std::basic_streambuf<_CharT, _Traits>::operator=(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits]’ is private
operator=(const basic_streambuf& _sb)
^
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4:0,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:36:51: error: within this context
std::streambuf::operator=(std::move(src));
^
/home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp: In member function ‘void shrinkwrap::stdio::filebuf::swap(shrinkwrap::stdio::filebuf::self_type&)’:
/home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:45:9: error: ‘swap’ is not a member of ‘std::streambuf {aka std::basic_streambuf}’
std::streambuf::swap(src);
^
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/reader.hpp:14:0,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:7,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/s1r.hpp: In member function ‘std::fstream savvy::s1r::writer::close()’:
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/s1r.hpp:829:14: error: ‘std::fstream’ has no member named ‘swap’
ofs.swap(ret);
^
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/s1r.hpp:830:16: error: use of deleted function ‘std::basic_fstream::basic_fstream(const std::basic_fstream&)’
return ret;
^
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/s1r.hpp:14:0,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/reader.hpp:14,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:7,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/fstream:776:11: note: ‘std::basic_fstream::basic_fstream(const std::basic_fstream&)’ is implicitly deleted because the default definition would be ill-formed:
class basic_fstream : public basic_iostream<_CharT, _Traits>
^
/usr/include/c++/4.8.2/fstream:776:11: error: use of deleted function ‘std::basic_iostream::basic_iostream(const std::basic_iostream&)’
In file included from /usr/include/c++/4.8.2/iostream:40:0,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:7,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/istream:795:11: note: ‘std::basic_iostream::basic_iostream(const std::basic_iostream&)’ is implicitly deleted because the default definition would be ill-formed:
class basic_iostream
^
/usr/include/c++/4.8.2/istream:795:11: error: use of deleted function ‘std::basic_istream::basic_istream(const std::basic_istream&)’
/usr/include/c++/4.8.2/istream:58:11: note: ‘std::basic_istream::basic_istream(const std::basic_istream&)’ is implicitly deleted because the default definition would be ill-formed:
class basic_istream : virtual public basic_ios<_CharT, _Traits>
^
/usr/include/c++/4.8.2/istream:58:11: error: use of deleted function ‘std::basic_ios::basic_ios(const std::basic_ios&)’
In file included from /usr/include/c++/4.8.2/ios:44:0,
from /usr/include/c++/4.8.2/ostream:38,
from /usr/include/c++/4.8.2/iostream:39,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:7,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/bits/basic_ios.h:66:11: note: ‘std::basic_ios::basic_ios(const std::basic_ios&)’ is implicitly deleted because the default definition would be ill-formed:
class basic_ios : public ios_base
^
In file included from /usr/include/c++/4.8.2/streambuf:41:0,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:4,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/bits/ios_base.h:786:5: error: ‘std::ios_base::ios_base(const std::ios_base&)’ is private
ios_base(const ios_base&);
^
In file included from /usr/include/c++/4.8.2/ios:44:0,
from /usr/include/c++/4.8.2/ostream:38,
from /usr/include/c++/4.8.2/iostream:39,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:7,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/bits/basic_ios.h:66:11: error: within this context
class basic_ios : public ios_base
^
In file included from /usr/include/c++/4.8.2/iostream:40:0,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:7,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/istream:795:11: error: use of deleted function ‘std::basic_ostream::basic_ostream(const std::basic_ostream&)’
class basic_iostream
^
In file included from /usr/include/c++/4.8.2/iostream:39:0,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:7,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/ostream:58:11: note: ‘std::basic_ostream::basic_ostream(const std::basic_ostream&)’ is implicitly deleted because the default definition would be ill-formed:
class basic_ostream : virtual public basic_ios<_CharT, _Traits>
^
/usr/include/c++/4.8.2/ostream:58:11: error: use of deleted function ‘std::basic_ios::basic_ios(const std::basic_ios&)’
In file included from /usr/include/c++/4.8.2/iostream:40:0,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:7,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/istream:795:11: error: use of deleted function ‘std::basic_ios::basic_ios(const std::basic_ios&)’
class basic_iostream
^
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/s1r.hpp:14:0,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/reader.hpp:14,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:7,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/fstream:776:11: error: use of deleted function ‘std::basic_ios::basic_ios(const std::basic_ios&)’
class basic_fstream : public basic_iostream<_CharT, _Traits>
^
/usr/include/c++/4.8.2/fstream:776:11: error: use of deleted function ‘std::basic_filebuf::basic_filebuf(const std::basic_filebuf&)’
/usr/include/c++/4.8.2/fstream:72:11: note: ‘std::basic_filebuf::basic_filebuf(const std::basic_filebuf&)’ is implicitly deleted because the default definition would be ill-formed:
class basic_filebuf : public basic_streambuf<_CharT, _Traits>
^
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/stdio.hpp:4:0,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/shrinkwrap/istream.hpp:4,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/recombination.hpp:6,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/streambuf:802:7: error: ‘std::basic_streambuf<_CharT, _Traits>::basic_streambuf(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits]’ is private
basic_streambuf(const basic_streambuf& _sb)
^
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/s1r.hpp:14:0,
from /home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/reader.hpp:14,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:7,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/usr/include/c++/4.8.2/fstream:72:11: error: within this context
class basic_filebuf : public basic_streambuf<CharT, Traits>
^
In file included from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:8:0,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/writer.hpp: In destructor ‘virtual savvy::writer::~writer()’:
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/writer.hpp:241:42: error: use of deleted function ‘std::basic_fstream::basic_fstream(const std::basic_fstream&)’
auto idx_fs = index_file->close();
^
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp: In member function ‘bool dosage_writer::write_dosages(const full_dosages_results&, const std::vector<target_variant>&, const std::vector<target_variant>&, std::pair<long unsigned int, long unsigned int>, const reduced_haplotypes&, const region&)’:
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:407:15: error: no match for ‘operator=’ (operand types are ‘savvy::variant’ and ‘savvy::site_info’)
out_var = savvy::site_info(tar_only_it->chrom, tar_only_it->pos, tar_only_it->ref, {tar_only_it->alt}, tar_only_it->id);
^
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:407:15: note: candidates are:
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/reader.hpp:10:0,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:7,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: savvy::variant& savvy::variant::operator=(const savvy::variant&)
class variant : public site_info
^
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: no known conversion for argument 1 from ‘savvy::site_info’ to ‘const savvy::variant&’
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: savvy::variant& savvy::variant::operator=(savvy::variant&&)
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: no known conversion for argument 1 from ‘savvy::site_info’ to ‘savvy::variant&&’
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:440:13: error: no match for ‘operator=’ (operand types are ‘savvy::variant’ and ‘savvy::site_info’)
out_var = savvy::site_info(ref_it->chrom, ref_it->pos, ref_it->ref, {ref_it->alt}, ref_it->id);
^
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:440:13: note: candidates are:
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/reader.hpp:10:0,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:7,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: savvy::variant& savvy::variant::operator=(const savvy::variant&)
class variant : public site_info
^
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: no known conversion for argument 1 from ‘savvy::site_info’ to ‘const savvy::variant&’
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: savvy::variant& savvy::variant::operator=(savvy::variant&&)
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: no known conversion for argument 1 from ‘savvy::site_info’ to ‘savvy::variant&&’
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:451:21: error: no match for ‘operator=’ (operand types are ‘savvy::variant’ and ‘savvy::site_info’)
out_var_emp = savvy::site_info(ref_it->chrom, ref_it->pos, ref_it->ref, {ref_it->alt}, ref_it->id);
^
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:451:21: note: candidates are:
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/reader.hpp:10:0,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:7,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: savvy::variant& savvy::variant::operator=(const savvy::variant&)
class variant : public site_info
^
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: no known conversion for argument 1 from ‘savvy::site_info’ to ‘const savvy::variant&’
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: savvy::variant& savvy::variant::operator=(savvy::variant&&)
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: no known conversion for argument 1 from ‘savvy::site_info’ to ‘savvy::variant&&’
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:485:13: error: no match for ‘operator=’ (operand types are ‘savvy::variant’ and ‘savvy::site_info’)
out_var = savvy::site_info(tar_only_it->chrom, tar_only_it->pos, tar_only_it->ref, {tar_only_it->alt}, tar_only_it->id);
^
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:485:13: note: candidates are:
In file included from /home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/reader.hpp:10:0,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/unique_haplotype.hpp:7,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.hpp:5,
from /home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:1:
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: savvy::variant& savvy::variant::operator=(const savvy::variant&)
class variant : public site_info
^
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: no known conversion for argument 1 from ‘savvy::site_info’ to ‘const savvy::variant&’
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: savvy::variant& savvy::variant::operator=(savvy::variant&&)
/home/hunau/mahj/anaconda3/envs/py3.11/include/savvy/site_info.hpp:217:11: note: no known conversion for argument 1 from ‘savvy::site_info’ to ‘savvy::variant&&’
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp: In member function ‘void dosage_writer::set_format_fields(savvy::variant&, savvy::compressed_vector&)’:
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:752:78: error: ‘plus_eov’ is not a member of ‘savvy’
savvy::stride_reduce(sparse_dosages, sparse_dosages.size() / n_samples, savvy::plus_eov());
^
/home/hunau/mahj/chicken/imputation_vcf_1/minimac_impute/Minimac4-master/src/dosage_writer.cpp:752:94: error: expected primary-expression before ‘float’
savvy::stride_reduce(sparse_dosages, sparse_dosages.size() / n_samples, savvy::plus_eov());
^
make[2]: *** [CMakeFiles/minimac4.dir/src/dosage_writer.cpp.o] Error 1
make[1]: *** [CMakeFiles/minimac4.dir/all] Error 2
make: *** [all] Error 2
Binary created at /release-build/minimac4

[jonathonl]

The install.sh script should no longer be used (should have been deleted). Instead follow the instructions in the README to build from source. You will likely need to use a gcc version >= 5.

Instead of building from source, I recommend using the pre-built executable that can be installed by running https://github.com/statgen/Minimac4/releases/download/v4.1.2/minimac4-4.1.2-Linux-x86_64.sh.