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Santy-8128 / Minimac3

Minimac3 is a low memory and computationally efficient implementation of the genotype imputation algorithms. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
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Error when 'make' #16

Open nienkevanunen opened 2 years ago

nienkevanunen commented 2 years ago

Get this with both cloning the repo and downloading the tar from ftp://share.sph.umich.edu/minimac3/Minimac3.v2.0.1.tar.gz.

On Fedora 29.

...
g++  -std=c++0x -O4 -pipe -Wall -Werror  -Wno-strict-overflow -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall -Werror  -Wno-strict-overflow -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\""
Chromosome.cpp: In constructor ‘Chromosome::Chromosome(const string&, unsigned int, bool)’:
Chromosome.cpp:42:15: error: ‘*<unknown>.Chromosome::gs’ is used uninitialized in this function [-Werror=uninitialized]
     if (this->gs) delete gs;
         ~~~~~~^~
cc1plus: all warnings being treated as errors
make[3]: *** [../Makefiles/Makefile.common:81: obj/Chromosome.o] Error 1
make[2]: *** [Makefiles/Makefile.base:15: general] Error 2
make[1]: *** [../Library/libStatGenForMinimac3/Makefiles/Makefile.ext:50: ../Library/libStatGenForMinimac3/libStatGen.a] Error 2
make[1]: Leaving directory '/vol/projects/BIIM_guest/meta_cQTL/Lyme_cQTL/Minimac3/src'
make: *** [Library/libStatGenForMinimac3/Makefiles/Makefile.base:15: src] Error 2
steffenom commented 2 years ago

I had a similar issue. Building worked with make CFLAGS="-Wno-error=format-truncation". I haven't used Minimac3 yet, so I'm not sure whether my solution really works.

1 and #8 refer to similar problems. As suggested there, it might also work to replace libStatGenForMinimac3 in Minimac3/Library with the newest version of libStatGen.