Minimac4 install failed

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.

May 24 '21 07:05 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.

May 24 '21 11:05 jonathonl

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

May 24 '21 11:05 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.

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

May 24 '21 12:05 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.

May 24 '21 12:05 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.

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

May 24 '21 13:05 xiaomiyang36

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

May 24 '21 14:05 jonathonl

prefix=/

This does work. Than you very much!!!

May 25 '21 01:05 xiaomiyang36

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

Apr 23 '23 12:04 tragic-comedy

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.

Apr 23 '23 13:04 jonathonl