Error in getopt(spec = spec, opt = args) : long flag "start" is invalid

[gauri-nagavkar]

I am using SAIGE 1.0.9 and running step2_SPAtests.R. Here is the log:

R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)
Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so
locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] data.table_1.13.6      optparse_1.7.3         RhpcBLASctl_0.21-247.1
[4] SAIGE_1.0.9           
loaded via a namespace (and not attached):
[1] compiler_4.0.4     Matrix_1.3-2       Rcpp_1.0.7         getopt_1.20.3     
[5] grid_4.0.4         RcppParallel_5.1.6 lattice_0.20-41   
Usage: /usr/local/bin/step2_SPAtests.R [options]
/usr/local/bin/step2_SPAtests.R: error: Error in getopt(spec = spec, opt = args) : long flag "start" is invalid

Thanks!

[weizhou0]

Hi @gauri-nagavkar,

Can you double check if the newest version of step2_SPAtests.R is used?

Thanks, Wei

[gauri-nagavkar]

Hi @weizhou0, thanks for your comment! It looks like --start was an argument in the previous version, but has been removed in the latest version. Could you please point me to the change log that I can use to understand what has changed between different versions? Thank you so much!