BGI-shenzhen / PopLDdecay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
MIT License
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Fail to install when make file #1

Closed Yiguan closed 6 years ago

Yiguan commented 7 years ago

I followed the instruction to make file on MacOS, and an error was issued when I type 'make': It begun like this: ############

g++  -c  LD_Decay.cpp -o ../bin/LD_Decay.o    -L./include/gzstream/ -L./include/zlib/ 
clang: warning: argument unused during compilation: '-L./include/gzstream/'
clang: warning: argument unused during compilation: '-L./include/zlib/'
In file included from LD_Decay.cpp:5:
./FileDeal.h:390:1: warning: control may reach end of non-void function
      [-Wreturn-type]
}
^
./FileDeal.h:1221:1: warning: control may reach end of non-void function
      [-Wreturn-type]
}
^
LD_Decay.cpp:220:2: warning: 'delete' applied to a pointer that was allocated
      with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete All_Stat ;
        ^
              []
LD_Decay.cpp:203:24: note: allocated with 'new[]' here
        StarRsult *All_Stat = new StarRsult [((paraFA04->InInt)+1)];
                              ^
.................
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [../bin/PopLDdecay] Error 1

################ I don't know where is the problem. THanks!

cfljam commented 7 years ago

for me the gz archive cannot be unzipped in either linux

tar -zxvf PopLDdecay3.27.tar.gz

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

or osx

$ tar -zxvf PopLDdecay3.27.tar.gz 
tar: Unrecognized archive format
tar: Error exit delayed from previous errors.
hewm2008 commented 7 years ago

@cfljam I have Re-uploaded the XX.tar.gz but i also check gzip -t it. it is ok gzip file . you can re-download it and try again .
I had downloaded it by myself and installed it is ok now. so please check your files download files completed

cfljam commented 7 years ago

Many thanks!

Tool is working VERY Nicely thank you

Is there a citation for this tool?

On 15/06/2017, at 9:17 PM, hewm2008 notifications@github.com<mailto:notifications@github.com> wrote:

@cfljamhttps://github.com/cfljam I have Re-uploaded the XX.tar.gz but i also check gzip -t it. it is ok gzip file . you can re-download it and try again . I had downloaded it by myself and installed it is ok now. so please check your files download files completed

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hewm2008 commented 7 years ago

@cfljam @Yiguan As I knows to install on the macOS platform: step 1 : you must re-install two library 【lib and gzstream】

step 2 : Copy these two library into Dir PopLDdecay3.30/src/include/gzstream PopLDdecay3.30/src/include/zlib

step 3: sh make.sh

I hope this can help you.

zlib

If Lib [zlib] do not work you can download form this website and install it http://www.zlib.net/

gzstream

If Lib [gzstream] do not work you can download form this website and install it http://www.cs.unc.edu/Research/compgeom/gzstream/

hewm2008 commented 7 years ago

@Yiguan For macOS

step1 :Should must re-install two library 【zlib and gzstream】

          see  [zlib and gzstream] website 

step2 : # Copy these two library into Dirs

          cp libz.a libz.so*  PopLDdecayXX/src/include/zlib
          cp libgzstream.a  PopLDdecayXX/src/include/gzstream

step3 :

          sh make.sh # or [make && make clean]