Merge pull request #256 from aghaynes/master

fix issues that have cropped up since the last version (of R and deps)
SwissClinicalTrialOrganisation · Nov 27, 2023 · f6423d2 · f6423d2
2 parents f0034ed + ef85893
commit f6423d2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,12 @@
 Package: secuTrialR
 Type: Package
 Title: Handling of Data from the Clinical Data Management System 'secuTrial'
-Version: 1.1.1
+Version: 1.2.0
 Authors@R:
     c(person(given = "Alan G.",
              family = "Haynes",
              role = c("cre", "aut", "cph"),
-             email = "alan.haynes@ctu.unibe.ch"),
+             email = "[email protected]"),
       person(given = "Patrick R.",
              family = "Wright",
              role = c("aut", "cph"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# secuTrialR 1.2.0
+
+* `write_secuTrial()` no longer allows `format = "sas"` due to deprecation of write_sas in `haven` (version 2.5.2).
+* `read_secuTrial_raw` now produces a more explicit warning when ISO-8859 encoding is used. Recent changes in R seem to have reduced compatibility with this encoding.
+
 # secuTrialR 1.1.1
 * fix CRAN notes - remove codecov badge, check class via inherits
 

diff --git a/R/read_export_table.R b/R/read_export_table.R
@@ -81,6 +81,7 @@ read_export_table <- function(data_dir, file_name, export_options,
   curr_encoding <- export_options$encoding
   if (curr_encoding == "ISO-8859-1" | curr_encoding == "ISO-8859-15") {
     curr_encoding <- "latin1"
+    warning("ISO-8859-1 encoding detected. Strings may not be interpreted correctly")
   }
 
   if (export_options$is_zip) {

diff --git a/R/write_secuTrial.R b/R/write_secuTrial.R
@@ -1,6 +1,6 @@
 #' Write secuTrial exports to other formats
 #' @description Convert the export prepared in R and export it to
-#'              SPSS (sav), Stata (dta) or SAS (sas, xpt version 8)
+#'              SPSS (sav), Stata (dta) or SAS (xpt version 8)
 #'              using the haven package.
 #' @name write_secuTrial
 #' @param object \code{secuTrialdata} object
@@ -27,12 +27,12 @@
 write_secuTrial <- function(object, ...) UseMethod("write_secuTrial", object)
 #' @export
 #' @name write_secuTrial
-#' @param format format in which to save the export (one of "dta", "sas", "sav", "xpt")
+#' @param format format in which to save the export (one of "dta", "sav", "xpt")
 #' @param metadata if TRUE then metadate files will also be written
 write_secuTrial.secuTrialdata <- function(object, format = "dta", metadata = FALSE, ...) {
 
-  if (! format %in% c("dta", "sas", "sav", "xpt")) {
-    stop(paste0("format must be one of 'dta', 'sas', 'sav', 'xpt'. You specified: ", format))
+  if (! format %in% c("dta", "sav", "xpt")) {
+    stop(paste0("format must be one of 'dta', 'sav', 'xpt'. You specified: ", format))
   }
   x <- object$export_options$data_names
   names(x) <- NULL
@@ -51,11 +51,9 @@ write_secuTrial.secuTrialdata <- function(object, format = "dta", metadata = FAL
 write_secuTrial.data.frame <- function(df, filename, path = "", format = "dta", ...) {
   df <- convertnames(df, format)
   format2 <- format
-  if (format == "sas") format2 <- "sas7bdat"
   out <- file.path(path, paste0(filename, ".", format2))
   if (format == "dta") haven::write_dta(df, out, ...)
   if (format == "sav") haven::write_sav(df, out, ...)
-  if (format == "sas") haven::write_sas(df, out, ...)
   if (format == "xpt") haven::write_xpt(df, out, version = 8, ...)
   paste("Saved to", out)
 }
diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 # secuTrialR
 
-[![](https://img.shields.io/badge/dev%20version-1.1.1-blue.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR)
+[![](https://img.shields.io/badge/dev%20version-1.2.0-blue.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR)
 [![](https://www.r-pkg.org/badges/version/secuTrialR?color=green)](https://cran.r-project.org/package=secuTrialR)
 [![AppVeyor Build
 Status](https://ci.appveyor.com/api/projects/status/github/SwissClinicalTrialOrganisation/secuTrialR?branch=master&svg=true)](https://ci.appveyor.com/project/SwissClinicalTrialOrganisation/secuTrialR)

diff --git a/man/write_secuTrial.Rd b/man/write_secuTrial.Rd
diff --git a/tests/testthat/test-dates_secutrial.R b/tests/testthat/test-dates_secutrial.R
@@ -220,7 +220,7 @@ path <- system.file("extdata", "sT_exports", "encodings",
                     "s_export_CSV-xls_TES05_short_ref_en_iso8859-15.zip",
                     package = "secuTrialR")
 
-tes05_raw <- read_secuTrial_raw(path)
+tes05_raw <- suppressWarnings(read_secuTrial_raw(path))
 
 test_that("loading data: TES05 incomplete dates (warn)", {
   expect_warning(f <- dates_secuTrial(tes05_raw, warn = TRUE))

diff --git a/tests/testthat/test-diff_secuTrial.R b/tests/testthat/test-diff_secuTrial.R
@@ -14,9 +14,10 @@ ctu05_en_2 <- read_secuTrial(system.file("extdata", "sT_exports", "snames",
 #> ctu05_en_2$export_options$project_version
 #[1] "(20.06.2019 - 11:22:04 (CEST))"
 
-ctu05_fr <- read_secuTrial(system.file("extdata", "sT_exports", "encodings",
-                                       "s_export_CSV-xls_CTU05_short_ref_miss_fr_iso8859-1.zip",
-                                       package = "secuTrialR"))
+ctu05_fr <- suppressWarnings(
+  read_secuTrial(system.file("extdata", "sT_exports", "encodings",
+                             "s_export_CSV-xls_CTU05_short_ref_miss_fr_iso8859-1.zip",
+                             package = "secuTrialR")))
 #> ctu05_fr$export_options$project_version
 #[1] "(20.06.2019 - 11:22:04 (CEST))"
 
@@ -70,3 +71,4 @@ test_that("Different version and changes", {
   expect_equal(length(v2_vs_v3$new_forms), 0)
   expect_equal(v2_vs_v3$new_variables, "yet_another_item")
 })
+
diff --git a/tests/testthat/test-encoding.R b/tests/testthat/test-encoding.R
@@ -25,9 +25,11 @@ exp_opt_ctu05_iso1_loc <- system.file("extdata", "sT_exports", "encodings",
 # utf8
 exp_opt_ctu05_utf8_eo <- read_export_options(exp_opt_ctu05_utf8_loc)
 # ISO-8859-15
-exp_opt_ctu05_iso15_eo <- read_export_options(exp_opt_ctu05_iso15_loc)
+exp_opt_ctu05_iso15_eo <- suppressWarnings(
+  read_export_options(exp_opt_ctu05_iso15_loc))
 # ISO-8859-1
-exp_opt_ctu05_iso1_eo <- read_export_options(exp_opt_ctu05_iso1_loc)
+exp_opt_ctu05_iso1_eo <- suppressWarnings(
+  read_export_options(exp_opt_ctu05_iso1_loc))
 
 # test encoding parser
 test_that("encodings parsed as expected", {
@@ -53,9 +55,9 @@ test_that("all export options outputs are equal", {
 # utf8
 exp_opt_ctu05_utf8_export <- read_secuTrial_raw(exp_opt_ctu05_utf8_loc)
 # ISO-8859-15
-exp_opt_ctu05_iso15_export <- read_secuTrial_raw(exp_opt_ctu05_iso15_loc)
+exp_opt_ctu05_iso15_export <- suppressWarnings(read_secuTrial_raw(exp_opt_ctu05_iso15_loc))
 # ISO-8859-1
-exp_opt_ctu05_iso1_export <- read_secuTrial_raw(exp_opt_ctu05_iso1_loc)
+exp_opt_ctu05_iso1_export <- suppressWarnings(read_secuTrial_raw(exp_opt_ctu05_iso1_loc))
 
 # nolint end
 
@@ -80,9 +82,12 @@ test_that("UTF-8 + BOM is not supported", {
 # macroman
 # the parsed options are incorrect thus we disallow MacRoman
 test_that("MacRoman is not supported", {
-  expect_error(read_export_options(system.file("extdata", "sT_exports", "encodings",
-                                               "s_export_CSV-xls_CTU05_short_ref_miss_fr_macroman.zip",
-                                               package = "secuTrialR"))
+  expect_error(
+    suppressWarnings(
+      read_export_options(system.file("extdata", "sT_exports", "encodings",
+                                      "s_export_CSV-xls_CTU05_short_ref_miss_fr_macroman.zip",
+                                      package = "secuTrialR"))
+    )
   )
 })
 

diff --git a/tests/testthat/test-links_secuTrial.R b/tests/testthat/test-links_secuTrial.R
@@ -33,7 +33,7 @@ len_long <- links_secuTrial(sT_export_long, plot = FALSE)
 len_sep_ref <- links_secuTrial(sT_export_sep_ref, plot = FALSE)
 
 test_that("igraph structure", {
-  expect_equal(len_short, len_short)
-  expect_equal(len_short, 310)
-  expect_equal(len_sep_ref, 1266)
+  expect_equal(len_short, len_long)
+  expect_equal(len_short, 170)
+  expect_equal(len_sep_ref, 666)
 })
diff --git a/tests/testthat/test-plot_recruitment.R b/tests/testthat/test-plot_recruitment.R
@@ -12,9 +12,9 @@ ldat <- read_secuTrial(system.file("extdata", "sT_exports", "lnames",
 ctu05_utf8_french <- read_secuTrial(system.file("extdata", "sT_exports", "encodings",
                                                 "s_export_CSV-xls_CTU05_short_ref_miss_fr_utf8.zip",
                                                 package = "secuTrialR"))
-ctu05_iso15_french <- read_secuTrial(system.file("extdata", "sT_exports", "encodings",
+ctu05_iso15_french <- suppressWarnings(read_secuTrial(system.file("extdata", "sT_exports", "encodings",
                                                  "s_export_CSV-xls_CTU05_short_ref_miss_fr_iso8859-15.zip",
-                                                 package = "secuTrialR"))
+                                                 package = "secuTrialR")))
 
 only_col_names_export_location <- system.file("extdata", "sT_exports", "exp_opt",
                                               "s_export_CSV-xls_CTU05_only_column_names.zip",

diff --git a/tests/testthat/test-read_export_options.R b/tests/testthat/test-read_export_options.R
@@ -29,9 +29,9 @@ dup_meta <- read_export_options(system.file("extdata", "sT_exports", "lnames",
                                             package = "secuTrialR"))
 
 # ISO-8859-15
-exp_opt_tes05_iso <- read_export_options(system.file("extdata", "sT_exports", "encodings",
+exp_opt_tes05_iso <- suppressWarnings(read_export_options(system.file("extdata", "sT_exports", "encodings",
                                                      "s_export_CSV-xls_TES05_short_ref_en_iso8859-15.zip",
-                                                     package = "secuTrialR"))
+                                                     package = "secuTrialR")))
 
 # test encoding
 test_that("Encoding parsed as expected.", {

diff --git a/tests/testthat/test-write_secuTrial.R b/tests/testthat/test-write_secuTrial.R
@@ -12,79 +12,64 @@ tdir <- tempdir()
 
 test_that("writing", {
   expect_error(write_secuTrial(sdat, path = tdir, format = "dta"), regexp = NA)
-  expect_error(write_secuTrial(sdat, path = tdir, format = "sas"), regexp = NA)
   expect_error(write_secuTrial(sdat, path = tdir, format = "sav"), regexp = NA)
   expect_error(write_secuTrial(sdat, path = tdir, format = "xpt"), regexp = NA)
   expect_error(write_secuTrial(ldat, path = tdir, format = "dta"), regexp = NA)
-  expect_error(write_secuTrial(ldat, path = tdir, format = "sas"), regexp = NA)
   expect_error(write_secuTrial(ldat, path = tdir, format = "sav"), regexp = NA)
   expect_error(write_secuTrial(ldat, path = tdir, format = "xpt"), regexp = NA)
 })
 
 test_that("files exist", {
   expect_true(file.exists(file.path(tdir, paste0("treatment", ".dta"))))
-  expect_true(file.exists(file.path(tdir, paste0("treatment", ".sas7bdat"))))
   expect_true(file.exists(file.path(tdir, paste0("treatment", ".sav"))))
   expect_true(file.exists(file.path(tdir, paste0("treatment", ".xpt"))))
   expect_false(file.exists(file.path(tdir, paste0("cn", ".dta"))))
-  expect_false(file.exists(file.path(tdir, paste0("cn", ".sas7bdat"))))
   expect_false(file.exists(file.path(tdir, paste0("cn", ".sav"))))
   expect_false(file.exists(file.path(tdir, paste0("cn", ".xpt"))))
 
   expect_true(file.exists(file.path(tdir, paste0("ctu05treatment", ".dta"))))
-  expect_true(file.exists(file.path(tdir, paste0("ctu05treatment", ".sas7bdat"))))
   expect_true(file.exists(file.path(tdir, paste0("ctu05treatment", ".sav"))))
   expect_true(file.exists(file.path(tdir, paste0("ctu05treatment", ".xpt"))))
   expect_false(file.exists(file.path(tdir, paste0("casenodes", ".dta"))))
-  expect_false(file.exists(file.path(tdir, paste0("casenodes", ".sas7bdat"))))
   expect_false(file.exists(file.path(tdir, paste0("casenodes", ".sav"))))
   expect_false(file.exists(file.path(tdir, paste0("casenodes", ".xpt"))))
 })
 
 test_that("writing meta", {
   expect_error(write_secuTrial(sdat, path = tdir, format = "dta", metadata = TRUE), regexp = NA)
-  expect_error(write_secuTrial(sdat, path = tdir, format = "sas", metadata = TRUE), regexp = NA)
   expect_error(write_secuTrial(sdat, path = tdir, format = "sav", metadata = TRUE), regexp = NA)
   expect_error(write_secuTrial(sdat, path = tdir, format = "xpt", metadata = TRUE), regexp = NA)
   expect_error(write_secuTrial(ldat, path = tdir, format = "dta", metadata = TRUE), regexp = NA)
-  expect_error(write_secuTrial(ldat, path = tdir, format = "sas", metadata = TRUE), regexp = NA)
   expect_error(write_secuTrial(ldat, path = tdir, format = "sav", metadata = TRUE), regexp = NA)
   expect_error(write_secuTrial(ldat, path = tdir, format = "xpt", metadata = TRUE), regexp = NA)
 })
 
 test_that("files exist", {
   expect_true(file.exists(file.path(tdir, paste0("treatment", ".dta"))))
-  expect_true(file.exists(file.path(tdir, paste0("treatment", ".sas7bdat"))))
   expect_true(file.exists(file.path(tdir, paste0("treatment", ".sav"))))
   expect_true(file.exists(file.path(tdir, paste0("treatment", ".xpt"))))
   expect_true(file.exists(file.path(tdir, paste0("cn", ".dta"))))
-  expect_true(file.exists(file.path(tdir, paste0("cn", ".sas7bdat"))))
   expect_true(file.exists(file.path(tdir, paste0("cn", ".sav"))))
   expect_true(file.exists(file.path(tdir, paste0("cn", ".xpt"))))
 
   expect_true(file.exists(file.path(tdir, paste0("ctu05treatment", ".dta"))))
-  expect_true(file.exists(file.path(tdir, paste0("ctu05treatment", ".sas7bdat"))))
   expect_true(file.exists(file.path(tdir, paste0("ctu05treatment", ".sav"))))
   expect_true(file.exists(file.path(tdir, paste0("ctu05treatment", ".xpt"))))
   expect_true(file.exists(file.path(tdir, paste0("casenodes", ".dta"))))
-  expect_true(file.exists(file.path(tdir, paste0("casenodes", ".sas7bdat"))))
   expect_true(file.exists(file.path(tdir, paste0("casenodes", ".sav"))))
   expect_true(file.exists(file.path(tdir, paste0("casenodes", ".xpt"))))
 })
 
 # test file content
 write_secuTrial(sdat, format = "dta", path = tdir)
 write_secuTrial(sdat, format = "sav", path = tdir)
-write_secuTrial(sdat, format = "sas", path = tdir)
 write_secuTrial(sdat, format = "xpt", path = tdir)
 sdat_dta_bl <- read_dta(paste0(tdir, "/baseline.dta"))
 sdat_sav_bl <- read_sav(paste0(tdir, "/baseline.sav"))
-sdat_sas_bl <- read_sas(paste0(tdir, "/baseline.sas7bdat"))
 sdat_xpt_bl <- read_xpt(paste0(tdir, "/baseline.xpt"))
 
 test_that("Baseline weight data is equal exist", {
   expect_true(all.equal(as.vector(sdat_dta_bl$weight), as.vector(sdat_sav_bl$weight)))
-  expect_true(all.equal(as.vector(sdat_dta_bl$weight), as.vector(sdat_sas_bl$weight)))
   expect_true(all.equal(as.vector(sdat_dta_bl$weight), as.vector(sdat_xpt_bl$weight)))
   expect_true(all.equal(as.vector(sdat_dta_bl$weight), as.vector(sdat$baseline$weight)))
   expect_true(all.equal(as.vector(sdat_dta_bl$weight), as.vector(ldat$ctu05baseline$weight)))
@@ -93,4 +78,5 @@ test_that("Baseline weight data is equal exist", {
 # test error catch for non-included formats
 test_that("Format illegal", {
   expect_error(write_secuTrial(sdat, format = "thatsnotit", path = tdir))
+  expect_error(write_secuTrial(sdat, format = "sas", path = tdir))
 })