mskcc / facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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FACETS installs with errors in the beginning #106

Closed WortJohn closed 5 years ago

WortJohn commented 5 years ago

@veseshan I install facets according to the manual install_github("mskcc/facets", build_vignettes = TRUE) but it runs unsuccessfully, the following is the error:

> library(devtools)
> install_github("mskcc/facets", build_vignettes = TRUE)
Downloading GitHub repo mskcc/facets@master
from URL https://api.github.com/repos/mskcc/facets/zipball/master
Installation failed: error in running command

My environment is:

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /public/home/zhangsr/anaconda3/lib/R/lib/libRblas.so
LAPACK: /public/home/zhangsr/anaconda3/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] devtools_1.13.6

loaded via a namespace (and not attached):
[1] httr_1.3.1     compiler_3.5.1 R6_2.2.2       tools_3.5.1    withr_2.1.2   
[6] curl_3.2       memoise_1.1.0  git2r_0.23.0   digest_0.6.15 
veseshan commented 5 years ago

This error does not seem specific to facets but rather a devtools issue. Please check if you can use install_github on any other package available through github.

WortJohn commented 5 years ago

Thanks for your reply. I solve it through install_local