WGLab / GenGen

A set of software tools to facilitate GWAS analysis
http://gengen.openbioinformatics.org
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Problems installing on Windows 10 #4

Open ABGane opened 6 years ago

ABGane commented 6 years ago

Hello,

I've been trying to install GenGen on a device running Windows10. I downloaded GenGen v1.0.1 (tar.gz). I unpacked this using the Bash shell with tar xvfz gengen.tar.gz as suggested and navigated to the kext directory where I modified the Makefile by changing the one occurrence of kc.so to kc.dll (included below). When I enter make though I get the following error:

$ make gcc perl -MExtUtils::Embed -e ccopts -fPIC -c -o kc_wrap.o kc_wrap.c kc_wrap.c:1:0: warning: -fPIC ignored for target (all code is position independent) /* ---------------------------------------------------------------------------- ^ In file included from kc_wrap.c:731:0: C:/Octave/OCTAVE~1.1/lib/perl5/5.8/msys/CORE/perl.h:925:27: fatal error: netinet/in.h: No such file or directory

include <netinet/in.h>

                       ^

compilation terminated. make: *** [kc_wrap.o] Error 1

I was wondering if anyone else has had the same problem and whether anyone knows how to get this working? I have also tried installing the same package on a Ubuntu virtual machine without any success (both the old and newer versions).

Thanks for any help you can provide!

---- Edited Makefile ----

SHELL = /bin/sh .SUFFIXES: .c .o

Notes:

When compiling in Windows, change the "kc.so" below to "kc.dll". The "-fPIC" can be optionally omitted

When compiling in Mac OS X, change the "kc.so" below to "kc.dylib", and change "-shared" to "-dynamiclib"

When compiling in Solaris, change "gcc" to "cc"

CC = gcc LD = gcc CFLAGS = perl -MExtUtils::Embed -e ccopts -fPIC LDFLAGS = perl -MExtUtils::Embed -e ldopts ARCH = perl -MConfig -e 'print $$Config{archname}' VER = perl -MConfig -e 'print $$Config{version}'

kc.dll: kc_wrap.o kc.o $(LD) -shared -o $@ $^ $(LDFLAGS) mkdir -p $(VER) mkdir -p $(VER)/$(ARCH)/ mkdir -p $(VER)/$(ARCH)/auto/ mv $@ $(VER)/$(ARCH)/

clean: rm -f .o .so

kaichop commented 6 years ago

I suggest that you just use a Linux machine to use PennCNV (or use a VM in windows). It is very difficult to compile source code in Windows due to many dependencies that are not well supported in Windows.

On Wed, Mar 14, 2018 at 4:49 PM, ABGane notifications@github.com wrote:

Hello,

I've been trying to install GenGen on a device running Windows10. I downloaded GenGen v1.0.1 (tar.gz). I unpacked this using the Bash shell with tar xvfz gengen.tar.gz as suggested and navigated to the kext directory where I modified the Makefile by changing the one occurrence of kc.so to kc.dll (included below). When I enter make though I get the following error:

$ make gcc perl -MExtUtils::Embed -e ccopts -fPIC -c -o kc_wrap.o kc_wrap.c kc_wrap.c:1:0: warning: -fPIC ignored for target (all code is position independent) /* ------------------------------------------------------------

^ In file included from kc_wrap.c:731:0: C:/Octave/OCTAVE~1.1/lib/perl5/5.8/msys/CORE/perl.h:925:27: fatal error: netinet/in.h: No such file or directory include <netinet/in.h>

                   ^

compilation terminated. make: *** [kc_wrap.o] Error 1

I was wondering if anyone else has had the same problem and whether anyone knows how to get this working? I have also tried installing the same package on a Ubuntu virtual machine without any success (both the old and newer versions).

Thanks for any help you can provide!

---- Edited Makefile ----

SHELL = /bin/sh .SUFFIXES: .c .o Notes: When compiling in Windows, change the "kc.so" below to "kc.dll". The "-fPIC" can be optionally omitted When compiling in Mac OS X, change the "kc.so" below to "kc.dylib", and change "-shared" to "-dynamiclib" When compiling in Solaris, change "gcc" to "cc"

CC = gcc LD = gcc CFLAGS = perl -MExtUtils::Embed -e ccopts -fPIC LDFLAGS = perl -MExtUtils::Embed -e ldopts ARCH = perl -MConfig -e 'print $$Config{archname}' VER = perl -MConfig -e 'print $$Config{version}'

kc.dll: kc_wrap.o kc.o $(LD) -shared -o $@ $^ $(LDFLAGS) mkdir -p $(VER) mkdir -p $(VER)/$(ARCH)/ mkdir -p $(VER)/$(ARCH)/auto/ mv $@ $(VER)/$(ARCH)/

clean: rm -f .o .so

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