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Vivianstats / scImpute

Accurate and robust imputation of scRNA-seq data
https://www.nature.com/articles/s41467-018-03405-7
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Could not load the scImpute library in R after installation: Conflicts with other packages #16

Closed parichit closed 5 years ago

parichit commented 6 years ago

@Vivianstats : Thanks for developing the scImpute package. It appears to be really useful for imputing the scRNA data. I was trying to load the package and run it in my own test data and came across this error where the package could not be loaded by R. It appears to be a dependency conflict with other packages.

Can you please help in troubleshooting this error, better would be if this can be taken care of in the future releases of the package:

Output from RStudio R console:

library(scImpute)

Loading required package: doParallel Loading required package: foreach Error in value[3L] : Package ‘foreach’ version 1.4.3 cannot be unloaded: Error in unloadNamespace(package) : namespace ‘foreach’ is imported by ‘doSNOW’, ‘caret’, ‘Seurat’ so cannot be unloaded

Vivianstats commented 6 years ago

Hello parichit,

I was not able to reproduce the error, but it looks like a problem with different package versions. I would suggest that you update foreach to version 1.4.4 and other packages that depend on it. I'm attaching my output of sessionInfo() for your information:

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

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] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] scImpute_0.0.8    doParallel_1.0.11 iterators_1.0.9   foreach_1.4.4    
[5] penalized_0.9-50  survival_2.41-3   devtools_1.13.5  

loaded via a namespace (and not attached):
 [1] rsvd_0.9         Rcpp_0.12.17     codetools_0.2-15 lattice_0.20-35 
 [5] digest_0.6.15    withr_2.1.2      grid_3.4.2       R6_2.2.2        
 [9] git2r_0.21.0     httr_1.3.1       curl_3.2         kernlab_0.9-26  
[13] Matrix_1.2-14    splines_3.4.2    tools_3.4.2      compiler_3.4.2  
[17] memoise_1.1.0    knitr_1.20