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unable to install regtools #202

@uqwwon15

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@uqwwon15

Hi how are you? been trying to install regtools on HPC, but got this error message. Thank you


[ 1%] Building CXX object src/variants/CMakeFiles/variants.dir/variants_main.cc.o
In file included from /scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../utils/common.h:34,
from /scratch/project/genetic_data_analysis/cheong/regtools/src/variants/variants_main.cc:27:
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../utils/bedtools/bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../utils/bedtools/bedFile/bedFile.h:345:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
345 | for (register short i = 0; i < binLevels; ++i) {
| ^
In file included from /scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_annotator.h:35,
from /scratch/project/genetic_data_analysis/cheong/regtools/src/variants/variants_annotator.h:35,
from /scratch/project/genetic_data_analysis/cheong/regtools/src/variants/variants_main.cc:28:
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_extractor.h: In constructor ‘JunctionsExtractor::JunctionsExtractor(std::string, std::string, int, std::string, uint32_t, uint32_t, uint32_t, std::string)’:
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_extractor.h:180:16: warning: ‘JunctionsExtractor::strand_tag
’ will be initialized after [-Wreorder]
180 | string strand_tag_;
| ^~~~~~~~~~~
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_extractor.h:158:18: warning: ‘uint32_t JunctionsExtractor::min_anchor_length_’ [-Wreorder]
158 | uint32_t min_anchor_length_;
| ^~~~~~~~~~~~~~~~~~
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_extractor.h:199:9: warning: when initialized here [-Wreorder]
199 | JunctionsExtractor(string bam1, string region1, int strandness1, string strand_tag1, uint32_t min_anchor_length1, uint32_t min_intron_length1, uint32_t max_intron_length1, string ref1) :
| ^~~~~~~~~~~~~~~~~~
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_extractor.h:162:18: warning: ‘JunctionsExtractor::max_intron_length_’ will be initialized after [-Wreorder]
162 | uint32_t max_intron_length_;
| ^~~~~~~~~~~~~~~~~~
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_extractor.h:154:16: warning: ‘std::string JunctionsExtractor::ref_’ [-Wreorder]
154 | string ref_;
| ^~~~
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_extractor.h:199:9: warning: when initialized here [-Wreorder]
199 | JunctionsExtractor(string bam1, string region1, int strandness1, string strand_tag1, uint32_t min_anchor_length1, uint32_t min_intron_length1, uint32_t max_intron_length1, string ref1) :
| ^~~~~~~~~~~~~~~~~~
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_annotator.h: In constructor ‘JunctionsAnnotator::JunctionsAnnotator(std::string)’:
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_annotator.h:194:16: warning: ‘JunctionsAnnotator::output_file_’ will be initialized after [-Wreorder]
194 | string output_file_;
| ^~~~~~~~~~~~
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_annotator.h:184:17: warning: ‘BedFile JunctionsAnnotator::junctions_’ [-Wreorder]
184 | BedFile junctions_;
| ^~~~~~~~~~
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/../junctions/junctions_annotator.h:220:9: warning: when initialized here [-Wreorder]
220 | JunctionsAnnotator(string bedFile)
| ^~~~~~~~~~~~~~~~~~
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/variants_main.cc: In function ‘int variants_annotate(int, char**)’:
/scratch/project/genetic_data_analysis/cheong/regtools/src/variants/variants_main.cc:49:28: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
49 | } catch (runtime_error e) {
| ^
as: unrecognized option '--gdwarf-5'
make[2]: *** [src/variants/CMakeFiles/variants.dir/build.make:76: src/variants/CMakeFiles/variants.dir/variants_main.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:681: src/variants/CMakeFiles/variants.dir/all] Error 2
make: *** [Makefile:101: all] Error 2

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