Re: [wgs-assembler-users] Failure at the installation of the wgs-8.3

[A. B. C. <ber...@gm...>]

Hi Brian,
 Thank you.  It solved the problem in
cd kmer && make install && cd ..

 but we got an analogous error in the next step:

cd src && make && cd ..



          g++ -o
/home/bernardo/programs/wgs-8.3rc2/Linux-amd64/bin/buildRefContigs
/home/bernardo/programs/wgs-8.3rc2/Linux-amd64/obj/buildRefContigs.o
/home/bernardo/programs/wgs-8.3rc2/Linux-amd64/lib/libCA.a
-L/home/bernardo/programs/wgs-8.3rc2/Linux-amd64/lib
 -L/home/bernardo/programs/wgs-8.3rc2/Linux-amd64/lib
 -L/home/bernardo/programs/wgs-8.3rc2/kmer/Linux-amd64/lib  -L/usr/lib64
 -L/usr/X11R6/lib64 -D_GLIBCXX_PARALLEL -fopenmp -pthread -lm -Wl,-O1
-rdynamic
* Make Target is all
############################## AS_RUN ##############################
############################## AS_UTL ##############################
############################## AS_UID ##############################
############################## AS_MSG ##############################
############################## AS_PER ##############################
############################## AS_GKP ##############################
############################## AS_OBT ##############################
############################## AS_MER ##############################
############################## AS_OVL ##############################
############################## AS_OVM ##############################
############################## AS_OVS ##############################
############################## AS_ALN ##############################
############################## AS_CGB ##############################
############################## AS_BOG ##############################
############################## AS_BAT ##############################
############################## AS_PBR ##############################
make[1]: execvp: ln: Too many levels of symbolic links
Makefile:160: recipe for target 'PBcR' failed
make[1]: *** [PBcR] Error 127
make[1]: *** Waiting for unfinished jobs....
make[1]: *** wait: No child processes.  Stop.
Makefile:35: recipe for target 'all' failed
make: *** [all] Error 1


A. Bernardo Carvalho

Departamento de Genética
Universidade Federal do Rio de Janeiro

On 23 December 2015 at 04:14, Brian Walenz <th...@gm...> wrote:

> Hi-
>
> Edit kmer/Make.include to remove (or comment out) the two lines with
> 'atac-driver' and 'seatac' in them.  These aren't used by the assembler,
> and this will make 'make' (ha, ha) not build them.
>
> b
>
>
>
> On Tue, Dec 22, 2015 at 12:11 PM, gabriel goldstein <
> gnr...@gm...> wrote:
>
>> Hello,
>>
>> My name is Gabriel Goldstein and I'm trying to install the assembler in a
>> Ubuntu 15.04 system, with gcc 4.9.2 and GNU Make 4.0.
>> However, whenever I go into wgs-8.3rc2/kmer/ and use the command make
>> install I get the following error:
>>
>> ln -f
>> /home/bernardo/programs/wgs-8.3rc2/kmer/atac-driver/alignOverlap/overlap-process.C
>> /home/bernardo/programs/wgs-8. 3rc2/kmer/atac-driver/alignOverlap/overlap-process1.C
>> make: execvp: ln: Too many levels of symbolic links
>> atac-driver/alignOverlap/Make.include:29: recipe for target
>> 'atac-driver/alignOverlap/overlap-process1.C' failed
>> make: *** [atac-driver/alignOverlap/overlap-process1.C] Error 12
>>
>> I've tried using an older version of GNU Make (3.8), but the same problem
>> remains. Are there any known issues related with the new version of gcc?
>> This error message really tells me nothing, is it commom?
>>
>> Thanks in advance for the attention,
>>
>> Gabriel Goldstein
>>
>>
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