Cannot install

[shehongbing]

Hi,
i install the software as suggested. But it's failed. The error messages is followes:

/usr/bin/ld: build/common/lk_pade_table.o: undefined reference to symbol 'pthread_condattr_setclock@@GLIBC_2.3.3'
/usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make: *** [ldhelmet] Error 1

I wondering that if you have any suggestions. Or, can i install this by conda

THX
Hongbing

[Paul-Jenkins]

Dear Hongbing Thank you for your interest in our software. Unfortunately it's quite hard to diagnose an error message like this without having more information about the setup of your operating system. But my guess is that the programme is failing to link to boost correctly, probably because boost is installed to a different location than that expected by the compiler. You can specify to the compiler where your installed copy of boost is - there are some instructions on how to do this in the LDhelmet manual. You could also try compiling some other programme that uses boost to make sure that boost is installed correctly. Good luck! Paul

…

On Thu, 24 Aug 2023 at 05:53, shehongbing ***@***.***> wrote: Hi, i install the software as suggested. But it's failed. The error messages is followes: /usr/bin/ld: build/common/lk_pade_table.o: undefined reference to symbol 'pthread_condattr_setclock@@GLIBC_2.3.3' /usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make: *** [ldhelmet] Error 1 I wondering that if you have any suggestions. Or, can i install this by conda THX Hongbing — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADBXPZ74B2JW3UGQRPUBBO3XW3M6LANCNFSM6AAAAAA34NTZVI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[shehongbing]

Dear Paul,

Thanks for your kind help. I addressed this error as per suggested. I have another question. I only have VCF files with 138,771 variants of 6 chromosomes for 13 accessions. The SNPs format could be used in rjmcmc but not the find_confs. Then, I get sequences (fasta format) for each accession based on the SNP. I was wondering if this is a correct method. My commands are as followes:
(1) ## Chr1-6 contain fasta sequences of 13 accessions based on SNPs.
ldhelmet find_confs --num_threads 24 -w 5000 -o output/output.conf Chr1.fa Chr2.fa Chr3.fa Chr4.fa Chr5.fa Chr6.fa
(2) ## table_gen
ldhelmet table_gen --num_threads 24 -t 0.01 -r 0.0 0.1 10.0 1.0 100.0 -c output/output.conf -o output/output.lk
(3) ## pade
ldhelmet pade --num_threads 24 -c output/output.conf -t 0.01 -x 11 -o output/output.pade
(4) ##rjmcmc
for i in {1..6}
do
ldhelmet rjmcmc --num_threads 24 -l output/output.lk -p output/output.pade -s Chr${i} -w 5000 -b 50.0 --burn_in 100000 -n 1000000 -o output/output_chr${i}.post
done
(5) ## post_to_text
for i in {1..6}
do
ldhelmet post_to_text -m -p 0.025 -p 0.50 -p 0.975 -o output/output_chr${i}.txt output/output_chr${i}.post
done

After that, i will get the recombination rate.
Could you please give some suggestions for my analysis. Thank you very much

Best,
Hongbing

[atlashrike]

Hi,

Just adding that I had the same issue (WSL) and I solved it by modifying
LIB = -lboost_thread -lboost_program_options -lboost_system -lgsl -lgslcblas
in the Makefile to
LIB = -lboost_thread -lboost_program_options -lboost_system -lgsl -lgslcblas -lpthread.