Installing Vcftools And Architect Incompatibility !
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0
Entering edit mode
8.2 years ago
User 1933 ▴ 340

I tried to install vcftool on my ubuntu 10.04; so I downloaded the latest version from http://sourceforge.net/projects/vcftools/files/, and went to the folder and I typed "make"

make[1]: Entering directory `/home/superiois/Downloads/vcftools_0.1.11/cpp'
g++ -O2 -D_FILE_OFFSET_BITS=64  vcftools.o bcf_file.o vcf_file.o variant_file.o bcf_entry.o vcf_entry.o entry.o entry_setters.o entry_getters.o vcf_entry_setters.o    bcf_entry_setters.o variant_file_filters.o variant_file_output.o variant_file_format_convert.o variant_file_diff.o header.o parameters.o variant_file_index.o output_log.o bgzf.o gamma.o -o vcftools -lz 
variant_file_format_convert.o: In function `variant_file::output_as_012_matrix(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
variant_file_format_convert.cpp:(.text+0x26fb): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/usr/bin/ld: i386:x86-64 architecture of input file `bgzf.o' is incompatible with i386 output
collect2: ld returned 1 exit status
make[1]: *** [vcftools] Error 1
make[1]: Leaving directory `/home/superiois/Downloads/vcftools_0.1.11/cpp'
cd: 2: can't cd to perl
make: *** [install] Error 2

I don't think it is really an OS architect error ! since If I am not mistaken the vcftools is only provided in one format ! and my labtop is also 32bit. thanks for helping me on this issue

vcftools • 2.8k views
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3
Entering edit mode
8.2 years ago
lomereiter ▴ 470

Edit CFLAGS in cpp/Makefile. For your architecture, it should contain -m32 instead of -m64.

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Entering edit mode
8.2 years ago
Sam ★ 4.2k

It is complaining about the file bgzf.o was created for 64bit computer. As your computer is 32 bit, that might be problematic. To solve this problem, you can try:

make clean

then

make install

if that doesn't work, you will have to modify the MakeFile under cpp, but that will be more complicated. Try the above code first and see if that solve your problem.

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Entering edit mode

thanks - again, complained about the same thing - help me to modify the MakeFile please :-)

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Entering edit mode

You can try using lomereiter's method, that should work

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