Unable to install SweeD

[SowmyaPulapet]

Hello,
I am not being able to install SweeD in my Linux system. I cloned the repostiory from github and used the command make -f Makefile.gcc to install SweeD. However I am getting the following error message:

/usr/bin/ld: SweeD_CLR.o:/Tools/sweed/SweeD.h:128: multiple definition of ``VCF_header_lines'; SweeD.o:/Tools/sweed/SweeD.h:128: first defined here

/usr/bin/ld: SweeD_CLR.o:/Tools/sweed/SweeD.h:127: multiple definition of ``ploidy'; SweeD.o:/Tools/sweed/SweeD.h:127: first defined here

/usr/bin/ld: SweeD_CLR.o://Tools/sweed/SweeD.h:126: multiple definition of borderTol'; ```SweeD.o:/Tools/sweed/SweeD.h:126: first defined here

/usr/bin/ld: SweeD_CLR.o:/Tools/sweed/SweeD.h:124: multiple definition of linkage_disequilibrium'; SweeD.o:/Tools/sweed/SweeD.h:124: first defined here

/usr/bin/ld: SweeD_CLR.o:/Tools/sweed/SweeD.h:122: multiple definition of ``bits_in_16bits'; SweeD.o:/Tools/sweed/SweeD.h:122: first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile.gcc:17: SweeD] Error 1
`
Hope you would help me rectify the error.

Thanks in advance!

[alachins]

Hi, You can use the compile_rename_ALL.sh <https://github.com/alachins/sweed/blob/master/compile_rename_ALL.sh> script for this. Best regards, Nikos A.

…

On Sat, Oct 8, 2022 at 1:55 PM SowmyaPulapet ***@***.***> wrote: Hello, I am not being able to install SweeD in my Linux system. I cloned the repostiory from github and used the command make -f Makefile.gcc to install SweeD. However I am getting the following error message: /usr/bin/ld: SweeD_CLR.o:/Tools/sweed/SweeD.h:128: multiple definition of ``VCF_header_lines'; SweeD.o:/Tools/sweed/SweeD.h:128: first defined here /usr/bin/ld: SweeD_CLR.o:/Tools/sweed/SweeD.h:127: multiple definition of ``ploidy'; SweeD.o:/Tools/sweed/SweeD.h:127: first defined here /usr/bin/ld: SweeD_CLR.o://Tools/sweed/SweeD.h:126: multiple definition of borderTol'; ```SweeD.o:/Tools/sweed/SweeD.h:126: first defined here /usr/bin/ld: SweeD_CLR.o:/Tools/sweed/SweeD.h:124: multiple definition of linkage_disequilibrium'; SweeD.o:/Tools/sweed/SweeD.h:124: first defined here /usr/bin/ld: SweeD_CLR.o:/Tools/sweed/SweeD.h:122: multiple definition of ``bits_in_16bits'; SweeD.o:/Tools/sweed/SweeD.h:122: first defined here collect2: error: ld returned 1 exit status make: *** [Makefile.gcc:17: SweeD] Error 1 ` Hope you would help me rectify the error. Thanks in advance! — Reply to this email directly, view it on GitHub <#25>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALKWCTXALUESS4Y44V6X23WCFOMHANCNFSM6AAAAAARAHI2QQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Nikolaos Alachiotis

[SowmyaPulapet]

Hi @alachins,
I used the command ./compile_rename_ALL.sh in the sweed tool folder. But I am still getting errors. The error log is attached.
error log

[ala98412]

Hi @alachins, I used the command ./compile_rename_ALL.sh in the sweed tool folder. But I am still getting errors. The error log is attached. error log

Same problem here. Any solution?

Thanks.

[madzafv]

Same problem here.
I loaded gcc/6.5.0 and was able to compile the program.
-madza

[YuhengSun]

Hi,
You can use the compile_rename_ALL.sh
https://github.com/alachins/sweed/blob/master/compile_rename_ALL.sh
script for this.
Best regards,
Nikos A.
…

Hi. I've got the same problem, and it couldn't be fixed using this script.
I do not have early version gcc's so it hasn't been resolved.

[mgallantcanguilhem]

Have you tried just this line from the script : make -f Makefile.gcc && rm *.o;
It worked for me !