Error in collapse(tmp, inner = FALSE, indent = indent) : R character strings are limited to 2^31-1 bytes

[sigven]

Error in collapse(tmp, inner = FALSE, indent = indent) : R character strings are limited to 2^31-1 bytes

[sigven]

Dear Jianxiang,
Thanks a lot for reporting this! Would it be possible for you to share your input, as this is the likely cause for the bug (an un-anticipated type of input somewhere)?
regards,
Sigve

[jxshi]

Hi Sigve,

Here is the link to the vcf file that I used. I tried on two different severs and both failed with the same error. By the way, the shared link will expire in 7 days.

Thank you for you time!

All the best,

Jianxiang

[sigven]

Hi,

FYI: the VCF being linked is a VCF file with somatic calls (tumor sample + normal sample), i.e. as used for PCGR. CPSR requires germline calls as input.

[jxshi]

Hi,

Thank you for pointing that out. I will try later with germline VCF file.

Cheers!

Jianxiang

[xiaoqiwang19]

Has this problem been solved ? I had the same problem.