resolve R_LIBS issue on Slurm nodes during R CMD check

.Rbuildignore

@@ -1,5 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.Renviron$
 ^\.travis\.yml$
 ^cran-comments\.md
 ^release\.R

.Renviron

@@ -0,0 +1,2 @@
+# the check directory must be available to the Slurm nodes:
+TEMP=/nfs/scratch/

tests/testthat/test-slurm_apply.R

@@ -3,6 +3,7 @@ context("slurm_apply")
 
 SLURM = system('sinfo', ignore.stdout = TRUE, ignore.stderr = TRUE)
 SLURM_MSG = 'Only test on Slurm head node.'
+SLURM_OPTS = list(time = '1')
 
 Sys.setenv(R_TESTS = "")
 
@@ -18,14 +19,14 @@ ftest <- function(par_m, par_sd = 1, ...) {
     c(s_m = mean(samp), s_sd = sd(samp))
 }
 
-## slurm libraries
-#test0 <- function(i) Sys.getenv()
-#slurm_apply(test0, data.frame(i = c(0)), pkgs = c(), jobname = 'test0', nodes = 1, cpus_per_node = 1)
+# ## FIXME
+# saveRDS(Sys.getenv(), 'testthat_env.RDS')
+# slurm_apply(function (i) Sys.getenv(), data.frame(i = c(0)), pkgs = c(), jobname = 'test0', nodes = 1, cpus_per_node = 1)
 
 test_that("slurm_apply gives correct output", {
     if (SLURM) skip(SLURM_MSG)
     sjob <- slurm_apply(ftest, pars, jobname = "test1", nodes = 2, 
-                        cpus_per_node = 1)
+                        cpus_per_node = 1, slurm_options = SLURM_OPTS)
     res <- get_slurm_out(sjob, "table")
     res_raw <- get_slurm_out(sjob, "raw")
     cleanup_files(sjob)
@@ -37,7 +38,7 @@ test_that("slurm_apply gives correct output", {
 test_that("slurm_apply works with single parameter", {
     if (SLURM) skip(SLURM_MSG)
     sjob <- slurm_apply(ftest, pars[, 1, drop = FALSE], jobname = "test2", 
-                        nodes = 2, cpus_per_node = 1)
+                        nodes = 2, cpus_per_node = 1, slurm_options = SLURM_OPTS)
     res <- get_slurm_out(sjob, "table")
     cleanup_files(sjob)
     expect_equal(pars$par_m, res$s_m, tolerance = 0.01)  
@@ -46,7 +47,7 @@ test_that("slurm_apply works with single parameter", {
 test_that("slurm_apply works with single row", {
     if (SLURM) skip(SLURM_MSG)
     sjob <- slurm_apply(ftest, pars[1, ], nodes = 2, jobname = "test3",
-                        cpus_per_node = 1)
+                        cpus_per_node = 1, slurm_options = SLURM_OPTS)
     res <- get_slurm_out(sjob, "table")
     cleanup_files(sjob)
     expect_equal(sjob$nodes, 1)
@@ -56,7 +57,8 @@ test_that("slurm_apply works with single row", {
 test_that("slurm_apply works with single parameter and single row", {
     if (SLURM) skip(SLURM_MSG)
     sjob <- slurm_apply(ftest, pars[1, 1, drop = FALSE], jobname = "test4",
-                        nodes = 2, cpus_per_node = 1)
+                        nodes = 2, cpus_per_node = 1,
+                        slurm_options = SLURM_OPTS)
     res <- get_slurm_out(sjob, "table")
     cleanup_files(sjob)
     expect_equal(pars$par_m[1], res$s_m, tolerance = 0.01)  
@@ -67,7 +69,8 @@ test_that("slurm_apply correctly handles add_objects", {
     sjob <- slurm_apply(function(i) ftest(pars[i, 1], pars[i, 2]),
                         data.frame(i = 1:nrow(pars)),
                         add_objects = c('ftest', 'pars'), jobname = "test5",
-                        nodes = 2, cpus_per_node = 1)
+                        nodes = 2, cpus_per_node = 1,
+                        slurm_options = SLURM_OPTS)
     res <- get_slurm_out(sjob, "table")
     cleanup_files(sjob)
     expect_equal(pars, res, tolerance = 0.01, check.attributes = FALSE)

tests/testthat/test-slurm_call.R

@@ -3,6 +3,7 @@ context("slurm_call")
 
 SLURM = system('sinfo', ignore.stdout = TRUE, ignore.stderr = TRUE)
 SLURM_MSG = 'Only test on Slurm head node.'
+SLURM_OPTS = list(time = '1')
 
 Sys.setenv(R_TESTS = "")
 
@@ -11,7 +12,7 @@ test_that("slurm_job name is correctly edited and output is correct", {
     z <- 0
     sjob <- slurm_call(function(x, y) x * 2 + y + z, list(x = 5, y = 6),
                        add_objects = c('z'),
-                       jobname = "test^\\* call")
+                       jobname = "test^\\* call", slurm_options = SLURM_OPTS)
     res <- get_slurm_out(sjob)
     cleanup_files(sjob)
     expect_equal(sjob$jobname, "test_call")
@@ -27,7 +28,7 @@ test_that("slurm_call will handle a bytecoded function", {
             y = 0:100),
         formula = y ~ x)
     result_local <- do.call(lm, params)
-    sjob <- slurm_call(lm, params, slurm_options = list(partition = 'sesynctest'))
+    sjob <- slurm_call(lm, params, slurm_options = SLURM_OPTS)
     result_slurm <- get_slurm_out(sjob)
     cleanup_files(sjob)
     expect_equal(result_slurm$coeficients, result_local$coeficients)