# Run this test for users to make sure the bioconductor package
# install feature of doAzureParallel are still working
context("bioconductor package install scenario test")
test_that("job single bioconductor package install Test", {
testthat::skip("Live test")
testthat::skip_on_travis()
credentialsFileName <- "credentials.json"
clusterFileName <- "cluster.json"
doAzureParallel::generateCredentialsConfig(credentialsFileName)
doAzureParallel::generateClusterConfig(clusterFileName)
# set your credentials
doAzureParallel::setCredentials(credentialsFileName)
cluster <- doAzureParallel::makeCluster(clusterFileName)
doAzureParallel::registerDoAzureParallel(cluster)
opt <- list(wait = TRUE)
'%dopar%' <- foreach::'%dopar%'
bioconductor <- 'AMOUNTAIN'
res <-
foreach::foreach(
i = 1:4,
bioconductor = bioconductor,
.options.azure = opt
) %dopar% {
"AMOUNTAIN" %in% rownames(installed.packages())
}
# verify the job result is correct
testthat::expect_equal(length(res),
4)
testthat::expect_equal(res,
list(TRUE, TRUE, TRUE, TRUE))
})
test_that("job multiple bioconductor package install Test", {
testthat::skip("Live test")
testthat::skip_on_travis()
credentialsFileName <- "credentials.json"
clusterFileName <- "cluster.json"
doAzureParallel::generateCredentialsConfig(credentialsFileName)
doAzureParallel::generateClusterConfig(clusterFileName)
# set your credentials
doAzureParallel::setCredentials(credentialsFileName)
cluster <- doAzureParallel::makeCluster(clusterFileName)
doAzureParallel::registerDoAzureParallel(cluster)
opt <- list(wait = TRUE)
'%dopar%' <- foreach::'%dopar%'
bioconductor <- c('AgiMicroRna', 'biobroom', 'BiocParallel')
res <-
foreach::foreach(i = 1:4,
bioconductor = bioconductor,
.options.azure = opt) %dopar% {
c("AgiMicroRna" %in% rownames(installed.packages()),
"biobroom" %in% rownames(installed.packages()),
"BiocParallel" %in% rownames(installed.packages()))
}
# verify the job result is correct
testthat::expect_equal(length(res),
4)
testthat::expect_equal(res,
list(
c(TRUE, TRUE, TRUE),
c(TRUE, TRUE, TRUE),
c(TRUE, TRUE, TRUE),
c(TRUE, TRUE, TRUE)))
})
test_that("pool multiple bioconductor package install Test", {
testthat::skip("Live test")
testthat::skip_on_travis()
credentialsFileName <- "credentials.json"
clusterFileName <- "cluster.json"
doAzureParallel::generateCredentialsConfig(credentialsFileName)
doAzureParallel::generateClusterConfig(clusterFileName)
config <- jsonlite::fromJSON(clusterFileName)
config$name <- "bioconductorPackages1"
config$poolSize$dedicatedNodes$min <- 0
config$poolSize$dedicatedNodes$max <- 0
config$poolSize$lowPriorityNodes$min <- 1
config$poolSize$lowPriorityNodes$max <- 1
config$rPackages$bioconductor <- c('AgiMicroRna', 'biobroom', 'BiocParallel')
configJson <- jsonlite::toJSON(config, auto_unbox = TRUE, pretty = TRUE)
write(configJson, file = paste0(getwd(), "/", clusterFileName))
# set your credentials
doAzureParallel::setCredentials(credentialsFileName)
cluster <- doAzureParallel::makeCluster(clusterFileName)
doAzureParallel::registerDoAzureParallel(cluster)
'%dopar%' <- foreach::'%dopar%'
res <-
foreach::foreach(i = 1:2) %dopar% {
c("AgiMicroRna" %in% rownames(installed.packages()),
"biobroom" %in% rownames(installed.packages()),
"BiocParallel" %in% rownames(installed.packages()))
}
# verify the job result is correct
testthat::expect_equal(length(res),
2)
testthat::expect_equal(res,
list(
c(TRUE, TRUE, TRUE),
c(TRUE, TRUE, TRUE)))
})
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