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saigegit / SAIGE

Development for SAIGE and SAIGE-GENE(+)
GNU General Public License v3.0
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SAIGE installation error #131

Open Sirtx opened 8 months ago

Sirtx commented 8 months ago

Hello,

I'm trying to install SAGE to an HPC environment, and all preparation steps seem to go well but the SAIGE's install command is always unsuccessful, and results in following error:

 (base) [user@HPC software]$ R CMD INSTALL SAIGE
* installing to library ‘/homes/user/R/x86_64-pc-linux-gnu-library/4.1’
* installing *source* package ‘SAIGE’ ...
** using staged installation
Usage: cget [OPTIONS] COMMAND [ARGS]...

Error: No such command "ignore".
ERROR: configuration failed for package ‘SAIGE’
* removing ‘/homes/user/R/x86_64-pc-linux-gnu-library/4.1/SAIGE’

I don't seem to find anything similar from the Github issue, or by Googling, so doesanyone know what package/software the error with "ignore" could be?

kscott-1 commented 8 months ago

It most likely has to do with cget and the following line :

https://github.com/saigegit/SAIGE/blob/1fa4a0bb9f940d9fe0726c943c5b3202dbdbaca4/configure#L21