Error faced in executables storing during Blat installation

Question

[sabreenaalam12345]

Hello,

I have created the directory MACHTYPE in home directory in bin. The variable of my MACHTYPE is x86_64-linux-gnu. To check whether my executables are storing in the directory I have tried to make fixCr by going to the directory Downloads/kent/src/utils/fixcr and typed make. The fixCr program did not come to the x86_64-linux-gnu directory. It says this whenever I type make

cc -O -g -o /home/sabreena/bin/x86_64/fixCr fixCr.o    ../../lib/x86_64/jkweb.a /usr/lib/x86_64-linux-gnu/libmysqlclient.a -ldl -lstdc++ -lrt  -lpthread /usr/lib/x86_64-linux-gnu/libssl.a -lcrypto ../../htslib/libhts.a -lpng16 -lm -lz 
  /home/linuxbrew/.linuxbrew/bin/ld: cannot open output file /home/sabreena/bin/x86_64/fixCr: No such file or directory
  collect2: error: ld returned 1 exit status
  make: *** [../../inc/userApp.mk:31: /home/sabreena/bin/x86_64/fixCr] Error 1

Why the output file cannot be opened? What's wrong here?

Answer 1

[Michael]

There may be an error in the setup or even in one Makefile, building Kent tools is not easy and error prone:

What happens if you run the following command directly:

cc -O -g -o /home/sabreena/bin/x86_64-linux-gnu/fixCr fixCr.o    ../../lib/x86_64/jkweb.a /usr/lib/x86_64-linux-gnu/libmysqlclient.a -ldl -lstdc++ -lrt  -lpthread /usr/lib/x86_64-linux-gnu/libssl.a -lcrypto ../../htslib/libhts.a -lpng16 -lm -lz 

I propose, you use the following machtype

 export MACHTYPE=x86_64 # without the linux-gnu suffix

and run the whole process again, including running a make clean and making directories if required.

[sabreenaalam12345]

Yes, I followed your advice and hence a long process took place. Now, it did not say the file cannot be opened but gave an another error.

collect2: error: ld returned 1 exit status make: *** [../../inc/userApp.mk:31: /home/sabreena/bin/x86_64/fixCr] Error 1

Why did this error come?

[Michael]

The relevant error message is the line above the output you gave, please give all the output.

[sabreenaalam12345]

This is the error message which came in loads, i just could provide a part of it due to the limitation of this text box..

/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x139d): undefined reference to `WPACKET_start_sub_packet_len__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x13ae): undefined reference to `WPACKET_set_flags'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x1452): undefined reference to `WPACKET_sub_memcpy__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x148e): undefined reference to `WPACKET_close'
/home/linuxbrew/.linuxbrew/bin/ld: /usr/lib/x86_64-linux-gnu/libssl.a(libssl-lib-statem_srvr.o): in function `tls_construct_server_certificate':
(.text+0x15cb): undefined reference to `WPACKET_put_bytes__'
/home/linuxbrew/.linuxbrew/bin/ld: /usr/lib/x86_64-linux-gnu/libssl.a(libssl-lib-statem_srvr.o): in function `tls_construct_new_session_ticket':
(.text+0x1966): undefined reference to `WPACKET_get_total_written'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x1988): undefined reference to `WPACKET_memcpy'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x199c): undefined reference to `WPACKET_memcpy'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x19bc): undefined reference to `WPACKET_reserve_bytes'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x19f5): undefined reference to `WPACKET_allocate_bytes'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x1e51): undefined reference to `WPACKET_memcpy'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x1e5f): undefined reference to `WPACKET_close'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x1f25): undefined reference to `WPACKET_put_bytes__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x1f43): undefined reference to `WPACKET_put_bytes__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x21bd): undefined reference to `WPACKET_allocate_bytes'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x21f9): undefined reference to `WPACKET_get_total_written'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x2243): undefined reference to `WPACKET_reserve_bytes'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x2286): undefined reference to `WPACKET_allocate_bytes'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x22a8): undefined reference to `WPACKET_close'
/home/linuxbrew/.linuxbrew/bin/ld: /usr/lib/x86_64-linux-gnu/libssl.a(libssl-lib-statem_srvr.o): in function `dtls_raw_hello_verify_request':
(.text+0x38cd): undefined reference to `WPACKET_put_bytes__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x38e4): undefined reference to `WPACKET_sub_memcpy__'
/home/linuxbrew/.linuxbrew/bin/ld: /usr/lib/x86_64-linux-gnu/libssl.a(libssl-lib-statem_srvr.o): in function `tls_construct_cert_status_body':
(.text+0x7300): undefined reference to `WPACKET_put_bytes__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x731f): undefined reference to `WPACKET_sub_memcpy__'
/home/linuxbrew/.linuxbrew/bin/ld: /usr/lib/x86_64-linux-gnu/libssl.a(libssl-lib-d1_lib.o): in function `DTLSv1_listen.part.0':
(.text+0x385): undefined reference to `WPACKET_init_static_len'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x39f): undefined reference to `WPACKET_put_bytes__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x3b8): undefined reference to `WPACKET_put_bytes__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x3d2): undefined reference to `WPACKET_memcpy'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x3e7): undefined reference to `WPACKET_start_sub_packet_len__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x401): undefined reference to `WPACKET_put_bytes__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x418): undefined reference to `WPACKET_put_bytes__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x42f): undefined reference to `WPACKET_put_bytes__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x446): undefined reference to `WPACKET_put_bytes__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x45b): undefined reference to `WPACKET_start_sub_packet_len__'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x484): undefined reference to `WPACKET_close'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x494): undefined reference to `WPACKET_close'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x4a9): undefined reference to `WPACKET_get_total_written'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x4b9): undefined reference to `WPACKET_finish'
/home/linuxbrew/.linuxbrew/bin/ld: (.text+0x892): undefined reference to `WPACKET_cleanup'
collect2: error: ld returned 1 exit status
make: *** [../../inc/userApp.mk:31: /home/sabreena/bin/x86_64/fixCr] Error 1

How should i solve the error?

[Michael]

Hi, there might be a version mismatch or missing library. I anticipate that it may be very hard or impossible to fix. In general BLAT doesn't use a modern build system and is terribly awkward to build from source (sorry, Jim). So there might be no reasonable way of installing it that way. Instead, please try to install it via bioconda https://bioconda.github.io/recipes/ucsc-blat/README.html

[sabreenaalam12345]

I did not understand what you meant.. Could you please elaborate?

[Michael]

Sorry, but it does not really matter. I guess it will be nearly impossible to debug the problem using this forum. Please try the bioconda recipe first and see where this leads.

[fabsassolas]

Actually I managed to find a fix for the same issue (undefined reference to WPACKET blabla) by installing a VM with Ubuntu 18.04 on it, if it can help you :)