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library(distcomp)
#> Loading required package: survival

## First we do the conventional thing.

uis <- readRDS("uis.RDS")
#> Warning in gzfile(file, "rb"): cannot open compressed file 'uis.RDS', probable
#> reason 'No such file or directory'
#> Error in gzfile(file, "rb"): cannot open the connection
coxOrig <- coxph(formula=Surv(time, censor) ~ age + becktota + ndrugfp1 + ndrugfp2 +
                     ivhx3 + race + treat + strata(site), data=uis)
#> Error in terms.formula(formula, specials = ss, data = data): object 'uis' not found
summary(coxOrig)
#> Error in summary(coxOrig): object 'coxOrig' not found

## We define the computation

coxDef <- data.frame(compType = names(availableComputations())[2],
                     formula = "Surv(time, censor) ~ age + becktota + ndrugfp1 + ndrugfp2 + ivhx3 + race + treat",
                     id = "UIS",
                     stringsAsFactors=FALSE)

library(opencpu)
#> Loading config from C:/Users/crame/Documents/R/win-library/3.6/opencpu/config/defaults.conf
#> Loading config from C:\Users\crame\AppData\Local\opencpu\opencpu/user.conf
#> Welcome to OpenCPU!
## We split the data by site
siteData <- with(uis, split(x=uis, f=site))
#> Error in with(uis, split(x = uis, f = site)): object 'uis' not found
nSites <- length(siteData)
#> Error in eval(expr, envir, enclos): object 'siteData' not found
# sites <- lapply(seq.int(nSites),
#                 function(x) list(name = paste0("site", x),
#                                  url = opencpu$url()))
sites <- lapply(seq_along(siteData),
                function(x) list(name = paste0("site", x),
                                 worker = makeWorker(defn = lmDef, data = siteData[[x]])
                ))
#> Error in lapply(seq_along(siteData), function(x) list(name = paste0("site", : object 'siteData' not found

ok <- Map(uploadNewComputation, sites,
          lapply(seq.int(nSites), function(i) coxDef),
          siteData)
#> Error in mapply(FUN = f, ..., SIMPLIFY = FALSE): object 'sites' not found

#stopifnot(all(as.logical(ok)))

master <- makeMaster(coxDef) #CoxMaster$new(defnId = coxDef$id, formula=coxDef$formula)

# for (site in sites) {
#   master$addSite(name = site$name, url = site$url)
# }
for (site in sites) {
  master$addSite(name = site$name, worker = site$worker)
}
#> Error in eval(expr, envir, enclos): object 'sites' not found

result <- master$run()
#> Error in master$run(): 'list' object cannot be coerced to type 'double'

master$summary()
#> Warning in master$summary(): Calculating...
#> Error in run(): could not find function "run"

print(master$summary(), digits=5)
#> Warning in master$summary(): Calculating...
#> Error in run(): could not find function "run"

sessionInfo()
#> R version 3.6.2 (2019-12-12)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 18362)
#> 
#> Matrix products: default
#> 
#> locale:
#> [1] LC_COLLATE=English_United States.1252 
#> [2] LC_CTYPE=English_United States.1252   
#> [3] LC_MONETARY=English_United States.1252
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.1252    
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] opencpu_2.1.5  distcomp_1.2   survival_3.1-8
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.3       compiler_3.6.2   pillar_1.4.2     later_1.0.0     
#>  [5] highr_0.8        tools_3.6.2      digest_0.6.23    jsonlite_1.6    
#>  [9] evaluate_0.14    tibble_2.1.3     lattice_0.20-38  pkgconfig_2.0.3 
#> [13] rlang_0.4.2      Matrix_1.2-18    shiny_1.4.0      parallel_3.6.2  
#> [17] yaml_2.2.0       xfun_0.12        fastmap_1.0.1    stringr_1.4.0   
#> [21] dplyr_0.8.3      httr_1.4.1       knitr_1.27       rappdirs_0.3.1  
#> [25] askpass_1.1      grid_3.6.2       tidyselect_0.2.5 glue_1.3.1      
#> [29] R6_2.4.1         rmarkdown_2.0    purrr_0.3.3      magrittr_1.5    
#> [33] webutils_1.0     promises_1.1.0   htmltools_0.4.0  splines_3.6.2   
#> [37] assertthat_0.2.1 mime_0.8         xtable_1.8-4     httpuv_1.5.2    
#> [41] stringi_1.4.4    openssl_1.4.1    crayon_1.3.4