From 11e664f2937713e553d03f186ffd90578c96391c Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Fri, 28 Jun 2024 20:34:01 +0100
Subject: [PATCH 01/48] Bump version

---
 DESCRIPTION | 2 +-
 NEWS.md     | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d80fffcc..db31af00 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: TwoSampleMR
 Title: Two Sample MR Functions and Interface to MR Base Database
-Version: 0.6.4
+Version: 0.6.5
 Authors@R: c(
     person("Gibran", "Hemani", , "g.hemani@bristol.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0920-1055")),
diff --git a/NEWS.md b/NEWS.md
index 1eddb855..d0c5d10d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# TwoSampleMR v0.6.5
+
+(Release date: 2024-##-##)
+
 # TwoSampleMR v0.6.4
 
 (Release date: 2024-06-05)

From 2c02618179dc673223cd82323390d85469692a38 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Fri, 28 Jun 2024 20:34:25 +0100
Subject: [PATCH 02/48] Bump roxygen2 version

---
 DESCRIPTION | 2 +-
 NEWS.md     | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index db31af00..efe14bee 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -69,4 +69,4 @@ Remotes:
     WSpiller/RadialMR
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/NEWS.md b/NEWS.md
index d0c5d10d..61e99638 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,7 @@
 
 (Release date: 2024-##-##)
 
+* Bumped version of roxygen2 for creating package documentation
 # TwoSampleMR v0.6.4
 
 (Release date: 2024-06-05)

From ded538afdad3c9b06605e7f72fb70ed6f1b97842 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Fri, 28 Jun 2024 20:36:20 +0100
Subject: [PATCH 03/48] Only test back to R version 4.3.2

---
 .github/workflows/check-full.yaml | 9 ++-------
 NEWS.md                           | 4 +++-
 2 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/check-full.yaml b/.github/workflows/check-full.yaml
index 4785740b..196eceba 100644
--- a/.github/workflows/check-full.yaml
+++ b/.github/workflows/check-full.yaml
@@ -25,9 +25,7 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
+          - {os: ubuntu-latest,   r: '4.3.2'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -48,10 +46,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: >
-            any::rcmdcheck,
-            randomForest=?ignore-before-r=4.1.0,
-            car=?ignore-before-r=4.4.0,
-            MendelianRandomization=?ignore-before-r=4.4.0
+            any::rcmdcheck
           needs: check
 
       - name: Create and populate .Renviron file
diff --git a/NEWS.md b/NEWS.md
index 61e99638..2db51dc9 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,7 +2,9 @@
 
 (Release date: 2024-##-##)
 
-* Bumped version of roxygen2 for creating package documentation
+* Bumped version of **roxygen2** for creating package documentation
+* Update the earliest version of R in the `R CMD check` GitHub Actions workflow to be 4.3.2. This is because the **meta** dependency depends on **lme4**, and the recent 1.1-35.4 release of **lme4** requires **Matrix** 1.6-2 which was released a few days after R 4.3.2.
+
 # TwoSampleMR v0.6.4
 
 (Release date: 2024-06-05)

From c41c745b3a17424ece90df06564825c36bb4518d Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 11:09:36 +0100
Subject: [PATCH 04/48] Re-enable tests requiring API

---
 tests/testthat/test_rsq.r | 36 ++++++++++++++++++++----------------
 1 file changed, 20 insertions(+), 16 deletions(-)

diff --git a/tests/testthat/test_rsq.r b/tests/testthat/test_rsq.r
index 9377b810..54e7addb 100644
--- a/tests/testthat/test_rsq.r
+++ b/tests/testthat/test_rsq.r
@@ -10,8 +10,9 @@ test_that("exposure data 1", {
 })
 
 test_that("exposure data 2", {
-  skip("Skip unless you have good access to the API.")
-  d <- extract_instruments(c('ieu-a-2', 'ieu-a-7')) %>% add_rsq()
+  d <- extract_instruments(c('ieu-a-2', 'ieu-a-7'))
+  if(inherits(d, "response")) skip("Server issues")
+  d <- d %>% add_rsq()
 	expect_true("rsq.exposure" %in% names(d))
 	expect_true("effective_n.exposure" %in% names(d))
 })
@@ -19,31 +20,34 @@ test_that("exposure data 2", {
 exposure <- exp_dat[1:5,]
 
 test_that("outcome data 1", {
-  skip("Skip unless you have good access to the API.")
-  d <- extract_outcome_data(exposure$SNP, 'ieu-a-2') %>% add_rsq()
+  d <- extract_outcome_data(exposure$SNP, 'ieu-a-2')
+  if(inherits(d, "response")) skip("Server issues")
+  d <- d %>% add_rsq()
 	expect_true("rsq.outcome" %in% names(d))
 	expect_true("effective_n.outcome" %in% names(d))
 })
 
 test_that("outcome data 2", {
-  skip("Skip unless you have good access to the API")
-  d <- extract_outcome_data(exposure$SNP, c('ieu-a-2', 'ieu-a-7')) %>% add_rsq()
+  d <- extract_outcome_data(exposure$SNP, c('ieu-a-2', 'ieu-a-7'))
+  if(inherits(d, "response")) skip("Server issues")
+  d <- d %>% add_rsq()
 	expect_true("rsq.outcome" %in% names(d))
 	expect_true("effective_n.outcome" %in% names(d))
 })
 
 test_that("dat 2", {
-  skip("Skip unless you have good access to the API.")
-  d <- make_dat(proxies=FALSE) %>% add_rsq()
+  d <- make_dat(proxies=FALSE)
+  if(inherits(d, "response")) skip("Server issues")
+  d <- d %>% add_rsq()
 	expect_true("rsq.outcome" %in% names(d) & "rsq.exposure" %in% names(d))
 	expect_true("effective_n.outcome" %in% names(d) & "effective_n.exposure" %in% names(d))
 })
 
 test_that("dat ukb-d", {
-  skip("Skip unless you have good access to the API.")
-  skip_on_ci()
   skip_on_cran()
-  d <- make_dat(exposure="ukb-d-30710_irnt", proxies=FALSE) %>% add_rsq()
+  d <- make_dat(exposure="ukb-d-30710_irnt", proxies=FALSE)
+  if(inherits(d, "response")) skip("Server issues")
+  d <- d %>% add_rsq()
 	expect_true("rsq.outcome" %in% names(d) & "rsq.exposure" %in% names(d))
 })
 
@@ -55,8 +59,8 @@ test_that("effective n", {
 })
 
 test_that("get_population_allele_frequency", {
-  skip("Skip unless you have good access to the API.")  
 	d <- extract_instruments("ieu-a-7")
+	if(inherits(d, "response")) skip("Server issues")
 	d <- add_metadata(d)
 	d$eaf.exposure.controls <- get_population_allele_frequency(
 		af = d$eaf.exposure,
@@ -68,16 +72,16 @@ test_that("get_population_allele_frequency", {
 })
 
 test_that("bbj-a-1", {
-  skip("Skip unless you have good access to the API.")
-  skip_on_ci()
   skip_on_cran()
-  d <- extract_instruments('bbj-a-1') %>% add_metadata() %>% add_rsq()
+  d <- extract_instruments('bbj-a-1')
+  if(inherits(d, "response")) skip("Server issues")
+  d <- d %>% add_metadata() %>% add_rsq()
 	expect_true(all(!is.na(d$rsq.exposure)))
 })
 
 test_that("bsen vs pn", {
-	skip("Skip unless you have good access to the API.")
   d <- extract_instruments("ieu-a-2")
+  if(inherits(d, "response")) skip("Server issues")
 	r1 <- get_r_from_bsen(d$beta.exposure, d$se.exposure, d$samplesize.exposure)
 	r2 <- get_r_from_pn(d$pval.exposure, d$samplesize.exposure)
 	expect_true(cor(abs(r1), r2) > 0.99)

From bda26e03074fa73134ab2b85d817d9b9a417d282 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 11:12:05 +0100
Subject: [PATCH 05/48] Re-enable tests requiring API

---
 tests/testthat/test_outcomes.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test_outcomes.R b/tests/testthat/test_outcomes.R
index a7f0008d..8144e290 100644
--- a/tests/testthat/test_outcomes.R
+++ b/tests/testthat/test_outcomes.R
@@ -2,27 +2,32 @@ context("outcome")
 
 test_that("outcomes", {
 
-  skip("Skip unless you have good access to the API.")
-  skip_on_ci()
   skip_on_cran()
 
 	a <- extract_instruments("ieu-a-7")
+	if(inherits(a, "response")) skip("Server issues")
 	b <- extract_outcome_data(a$SNP, "ieu-a-2", proxies=FALSE)
+	if(inherits(b, "response")) skip("Server issues")
 	expect_true(nrow(b) < 30 & nrow(b) > 15)
 
 	b <- extract_outcome_data(a$SNP, "ieu-a-2", proxies=TRUE)
+	if(inherits(b, "response")) skip("Server issues")
 	expect_true(nrow(b) > 30 & nrow(b) < nrow(a))
 
 	b <- extract_outcome_data(a$SNP, c("ieu-a-2", "a"), proxies=FALSE)
+	if(inherits(b, "response")) skip("Server issues")
 	expect_true(nrow(b) < 30 & nrow(b) > 15)
 
 	b <- extract_outcome_data(a$SNP, c("ieu-a-2", "a"), proxies=TRUE)
+	if(inherits(b, "response")) skip("Server issues")
 	expect_true(nrow(b) > 30 & nrow(b) < nrow(a))
 
 	b <- extract_outcome_data(a$SNP, c("ieu-a-2", "ieu-a-7"), proxies=FALSE)
+	if(inherits(b, "response")) skip("Server issues")
 	expect_true(nrow(b) > 60)
 
 	b <- extract_outcome_data(a$SNP, c("ieu-a-2", "ieu-a-7"), proxies=TRUE)
+	if(inherits(b, "response")) skip("Server issues")
 	expect_true(nrow(b) > 70)
 
 })

From bbb73c738898abd5c79a69a7353b1092662dc2f0 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 11:15:18 +0100
Subject: [PATCH 06/48] Re-enable tests requiring API

---
 tests/testthat/test_otherformats.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/testthat/test_otherformats.R b/tests/testthat/test_otherformats.R
index 21bcecaf..e6a16f09 100644
--- a/tests/testthat/test_otherformats.R
+++ b/tests/testthat/test_otherformats.R
@@ -12,8 +12,6 @@ test_that("MRInput", {
 })
 
 test_that("MRInput with cor", {
-  skip("Skip unless you have good access to the API.")
-  skip_on_ci()
   skip_on_cran()
 	expect_warning(w <- dat_to_MRInput(dat, get_correlations=TRUE)[[1]])
 	expect_true(nrow(w@correlation) == length(w@betaX))

From 3a8670cf0222153b3c093630abd258c73c11be29 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 11:17:08 +0100
Subject: [PATCH 07/48] Add API checks for future

---
 tests/testthat/test_ldsc.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/testthat/test_ldsc.R b/tests/testthat/test_ldsc.R
index 290a9796..4d8b9f19 100644
--- a/tests/testthat/test_ldsc.R
+++ b/tests/testthat/test_ldsc.R
@@ -4,7 +4,9 @@ context("LDSC")
 test_that("get afl2", {
 	skip("Very slow")
 	hm3info <- ieugwasr::afl2_list("hapmap3")
+	if(inherits(hm3info, "response")) skip("Server issues")
 	s <- ieugwasr::afl2_list()
+	if(inherits(s, "response")) skip("Server issues")
 	a <- ldsc_h2("ieu-a-2", snpinfo=hm3info)
 	b <- ldsc_rg("ieu-a-2", "ieu-a-2", snpinfo=hm3info)
 	c <- ldsc_rg("ukb-a-248", "ukb-b-19953", snpinfo=hm3info)

From f5d2e71f80818ab97bdb1bb0d66c84d8aa8a1aa0 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 11:22:10 +0100
Subject: [PATCH 08/48] Re-enable test requiring API

---
 tests/testthat/test_ld.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/testthat/test_ld.R b/tests/testthat/test_ld.R
index dccbc938..4af3dcba 100644
--- a/tests/testthat/test_ld.R
+++ b/tests/testthat/test_ld.R
@@ -1,10 +1,9 @@
 context("ld")
 
 test_that("extract some data", {
-  skip("Skip unless you have good access to the API.")
-  skip_on_ci()
   skip_on_cran()
   a <- extract_instruments(2, clump=FALSE)
+  if(inherits(a, "response")) skip("Server issues")
   out <- clump_data(a)
 })
 

From 47df9a306b0b5a87462146c469a852e1102a71a8 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 11:22:22 +0100
Subject: [PATCH 09/48] Remove a skip()

---
 tests/testthat/test_ld.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test_ld.R b/tests/testthat/test_ld.R
index 4af3dcba..13279aa3 100644
--- a/tests/testthat/test_ld.R
+++ b/tests/testthat/test_ld.R
@@ -37,7 +37,6 @@ test_that("clump multiple", {
 })
 
 test_that("clump local", {
-  skip("Skip unless you're GH running this test locally.")
 	skip_on_ci()
 	skip_on_cran()
 	skip_if_not(file.exists("/Users/gh13047/repo/opengwas-api-internal/opengwas-api/app/ld_files/EUR.bim"))

From cdb50f223bc7f66f748cb3179ac7ddcaca8db575 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 11:29:20 +0100
Subject: [PATCH 10/48] Add skip_on_ci()

---
 tests/testthat/test_add_metadata.r | 20 ++++++++++----------
 tests/testthat/test_instruments.R  |  2 +-
 tests/testthat/test_ld.R           |  3 ---
 tests/testthat/test_mvmr.R         |  3 ---
 tests/testthat/test_mvmr_local.R   |  1 -
 tests/testthat/test_otherformats.R |  1 +
 tests/testthat/test_outcomes.R     |  1 +
 tests/testthat/test_rsq.r          |  8 ++++++++
 8 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/tests/testthat/test_add_metadata.r b/tests/testthat/test_add_metadata.r
index 925c8c2e..9e47c227 100644
--- a/tests/testthat/test_add_metadata.r
+++ b/tests/testthat/test_add_metadata.r
@@ -18,64 +18,64 @@ context("add metadata")
 load(system.file("extdata", "test_add_metadata.RData", package="TwoSampleMR"))
 
 test_that("exposure data 1", {
-  skip("Skip unless you have good access to the API.")
+  skip_on_ci()
 	d1 <- d1 %>% add_metadata()
 	expect_true("units.exposure" %in% names(d1))
 })
 
 test_that("exposure data 2", {
-  skip("Skip unless you have good access to the API.")
+  skip_on_ci()
 	d2 <- d2 %>% add_metadata()
 	expect_true("units.exposure" %in% names(d2))
 })
 
 test_that("outcome data 1", {
-  skip("Skip unless you have good access to the API.")
+  skip_on_ci()
 	d3 <- d3 %>% add_metadata()
 	expect_true("units.outcome" %in% names(d3))
 })
 
 test_that("outcome data 2", {
-  skip("Skip unless you have good access to the API.")
+  skip_on_ci()
 	d4 <- d4 %>% add_metadata()
 	expect_true("units.outcome" %in% names(d4))
 })
 
 test_that("dat 2", {
-  skip("Skip unless you have good access to the API.")
+  skip_on_ci()
 	d5 <- d5 %>% add_metadata()
 	expect_true("units.outcome" %in% names(d5) & "units.exposure" %in% names(d5))
 })
 
 test_that("no id1", {
-  skip("Skip unless you have good access to the API.")
+  skip_on_ci()
 	d6$id.exposure <- "not a real id"
 	d6 <- add_metadata(d6)
 	expect_true(!"units.exposure" %in% names(d6))
 })
 
 test_that("no id2", {
-  skip("Skip unless you have good access to the API.")
+  skip_on_ci()
 	d7$id.outcome <- "not a real id"
 	d7 <- add_metadata(d7)
 	expect_true(!"units.outcome" %in% names(d7))
 })
 
 test_that("ukb-d", {
-  skip("Skip unless you have good access to the API.")
+  skip_on_ci()
 	d8 <- add_metadata(d8)
 	expect_true("units.outcome" %in% names(d8))
 })
 
 test_that("bbj-a-1", {
-  skip("Skip unless you have good access to the API.")
+  skip_on_ci()
 	d9 <- d9 %>% add_metadata()
 	expect_true("samplesize.exposure" %in% names(d9))
 	expect_true(all(!is.na(d9$samplesize.exposure)))
 })
 
 test_that("ieu-b-109", {
-  skip("Skip unless you have good access to the API.")
+  skip_on_ci()
 	d10 <- d10 %>% add_metadata()
 	expect_true("samplesize.exposure" %in% names(d10))
 	expect_true(all(!is.na(d10$samplesize.exposure)))
diff --git a/tests/testthat/test_instruments.R b/tests/testthat/test_instruments.R
index 222a470e..27c5cd13 100644
--- a/tests/testthat/test_instruments.R
+++ b/tests/testthat/test_instruments.R
@@ -2,7 +2,7 @@ context("Instruments")
 
 test_that("server and mrinstruments", {
 
-  skip("Skip unless you have good access to the API.")
+  skip_on_ci()
   
 	# no no
 	exp_dat <- extract_instruments(outcomes=c("ieu-a-1032"))
diff --git a/tests/testthat/test_ld.R b/tests/testthat/test_ld.R
index 13279aa3..267d8e1e 100644
--- a/tests/testthat/test_ld.R
+++ b/tests/testthat/test_ld.R
@@ -8,7 +8,6 @@ test_that("extract some data", {
 })
 
 test_that("clump", {
-  skip("Skip unless you have good access to the API.")
 	skip_on_ci()
 	skip_on_cran()
 	expect_equal(ncol(a), ncol(out))
@@ -18,7 +17,6 @@ test_that("clump", {
 
 
 test_that("matrix", {
-  skip("Skip unless you have good access to the API.")
 	skip_on_ci()
 	skip_on_cran()
 	b <- ld_matrix(out$SNP)
@@ -28,7 +26,6 @@ test_that("matrix", {
 
 
 test_that("clump multiple", {
-  skip("Skip unless you have good access to the API.")
 	skip_on_ci()
 	skip_on_cran()
 	a <- extract_instruments(c("ieu-a-2", "ieu-a-1001"), clump=FALSE)
diff --git a/tests/testthat/test_mvmr.R b/tests/testthat/test_mvmr.R
index e217db6b..4025fe25 100644
--- a/tests/testthat/test_mvmr.R
+++ b/tests/testthat/test_mvmr.R
@@ -1,7 +1,6 @@
 context("mvmr")
 
 test_that("control", {
-  skip("Skip unless you have good access to the API.")
 	skip_on_ci()
 	skip_on_cran()
 	lipids <- mv_extract_exposures(c("ieu-a-299","ieu-a-300","ieu-a-302"))
@@ -19,7 +18,6 @@ test_that("control", {
 
 
 test_that("dat", {
-  skip("Skip unless you have good access to the API.")
 	skip_on_ci()
 	skip_on_cran()
 	a <- mv_extract_exposures(c("ukb-b-5238", "ieu-a-1001"))
@@ -39,7 +37,6 @@ test_that("dat", {
 
 
 test_that("ordering", {
-  skip("Skip unless you have good access to the API.")
 	skip_on_ci()
 	skip_on_cran()
 	lipids1 <- mv_extract_exposures(c("ieu-a-299","ieu-a-300","ieu-a-302"))
diff --git a/tests/testthat/test_mvmr_local.R b/tests/testthat/test_mvmr_local.R
index 657cbb45..158d51ec 100644
--- a/tests/testthat/test_mvmr_local.R
+++ b/tests/testthat/test_mvmr_local.R
@@ -10,7 +10,6 @@ context("mvmr local")
 load(system.file("extdata", "test_add_mvmr_local.RData", package="TwoSampleMR"))
 
 test_that("mv exposure local", {
-  skip("Skip unless you have good access to the API.")
 	skip_on_ci()
 	skip_on_cran()
     f1 <- tempfile()
diff --git a/tests/testthat/test_otherformats.R b/tests/testthat/test_otherformats.R
index e6a16f09..e8fd11e5 100644
--- a/tests/testthat/test_otherformats.R
+++ b/tests/testthat/test_otherformats.R
@@ -13,6 +13,7 @@ test_that("MRInput", {
 
 test_that("MRInput with cor", {
   skip_on_cran()
+  skip_on_ci()
 	expect_warning(w <- dat_to_MRInput(dat, get_correlations=TRUE)[[1]])
 	expect_true(nrow(w@correlation) == length(w@betaX))
 })
diff --git a/tests/testthat/test_outcomes.R b/tests/testthat/test_outcomes.R
index 8144e290..d761acce 100644
--- a/tests/testthat/test_outcomes.R
+++ b/tests/testthat/test_outcomes.R
@@ -3,6 +3,7 @@ context("outcome")
 test_that("outcomes", {
 
   skip_on_cran()
+  skip_on_ci()
 
 	a <- extract_instruments("ieu-a-7")
 	if(inherits(a, "response")) skip("Server issues")
diff --git a/tests/testthat/test_rsq.r b/tests/testthat/test_rsq.r
index 54e7addb..1fb1b39b 100644
--- a/tests/testthat/test_rsq.r
+++ b/tests/testthat/test_rsq.r
@@ -10,6 +10,7 @@ test_that("exposure data 1", {
 })
 
 test_that("exposure data 2", {
+  skip_on_ci()
   d <- extract_instruments(c('ieu-a-2', 'ieu-a-7'))
   if(inherits(d, "response")) skip("Server issues")
   d <- d %>% add_rsq()
@@ -20,6 +21,7 @@ test_that("exposure data 2", {
 exposure <- exp_dat[1:5,]
 
 test_that("outcome data 1", {
+  skip_on_ci()
   d <- extract_outcome_data(exposure$SNP, 'ieu-a-2')
   if(inherits(d, "response")) skip("Server issues")
   d <- d %>% add_rsq()
@@ -28,6 +30,7 @@ test_that("outcome data 1", {
 })
 
 test_that("outcome data 2", {
+  skip_on_ci()
   d <- extract_outcome_data(exposure$SNP, c('ieu-a-2', 'ieu-a-7'))
   if(inherits(d, "response")) skip("Server issues")
   d <- d %>% add_rsq()
@@ -36,6 +39,7 @@ test_that("outcome data 2", {
 })
 
 test_that("dat 2", {
+  skip_on_ci()
   d <- make_dat(proxies=FALSE)
   if(inherits(d, "response")) skip("Server issues")
   d <- d %>% add_rsq()
@@ -45,6 +49,7 @@ test_that("dat 2", {
 
 test_that("dat ukb-d", {
   skip_on_cran()
+  skip_on_ci()
   d <- make_dat(exposure="ukb-d-30710_irnt", proxies=FALSE)
   if(inherits(d, "response")) skip("Server issues")
   d <- d %>% add_rsq()
@@ -59,6 +64,7 @@ test_that("effective n", {
 })
 
 test_that("get_population_allele_frequency", {
+  skip_on_ci()
 	d <- extract_instruments("ieu-a-7")
 	if(inherits(d, "response")) skip("Server issues")
 	d <- add_metadata(d)
@@ -73,6 +79,7 @@ test_that("get_population_allele_frequency", {
 
 test_that("bbj-a-1", {
   skip_on_cran()
+  skip_on_ci()
   d <- extract_instruments('bbj-a-1')
   if(inherits(d, "response")) skip("Server issues")
   d <- d %>% add_metadata() %>% add_rsq()
@@ -80,6 +87,7 @@ test_that("bbj-a-1", {
 })
 
 test_that("bsen vs pn", {
+  skip_on_ci()
   d <- extract_instruments("ieu-a-2")
   if(inherits(d, "response")) skip("Server issues")
 	r1 <- get_r_from_bsen(d$beta.exposure, d$se.exposure, d$samplesize.exposure)

From 3c6a3c20ac4b499cc8fabacd48e7397a2ea8ecea Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 11:38:41 +0100
Subject: [PATCH 11/48] Fix API condition

---
 tests/testthat/test_ld.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test_ld.R b/tests/testthat/test_ld.R
index 267d8e1e..99301ae3 100644
--- a/tests/testthat/test_ld.R
+++ b/tests/testthat/test_ld.R
@@ -3,7 +3,7 @@ context("ld")
 test_that("extract some data", {
   skip_on_cran()
   a <- extract_instruments(2, clump=FALSE)
-  if(inherits(a, "response")) skip("Server issues")
+  if(length(a) == 0) skip("Server issues")
   out <- clump_data(a)
 })
 

From 978d1e67dab5a854b4f4ce6921e121ed11cf02b1 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 11:43:03 +0100
Subject: [PATCH 12/48] Add skip_on_ci()

---
 tests/testthat/test_ld.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/testthat/test_ld.R b/tests/testthat/test_ld.R
index 99301ae3..caa7eaca 100644
--- a/tests/testthat/test_ld.R
+++ b/tests/testthat/test_ld.R
@@ -2,6 +2,7 @@ context("ld")
 
 test_that("extract some data", {
   skip_on_cran()
+  skip_on_ci()
   a <- extract_instruments(2, clump=FALSE)
   if(length(a) == 0) skip("Server issues")
   out <- clump_data(a)

From bee3f4335dd24c52e791e3da6156ebcb4333cf8d Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 21:02:07 +0100
Subject: [PATCH 13/48] Move skips to top of file

---
 tests/testthat/test_add_metadata.r | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/tests/testthat/test_add_metadata.r b/tests/testthat/test_add_metadata.r
index 9e47c227..4c30cce5 100644
--- a/tests/testthat/test_add_metadata.r
+++ b/tests/testthat/test_add_metadata.r
@@ -1,5 +1,10 @@
 context("add metadata")
 
+skip_if_offline()
+skip_if_offline(host = "api.opengwas.io")
+skip_on_cran()
+skip_on_ci()
+
 # get required data
 # d1 <- extract_instruments('ieu-a-2')
 # d2 <- extract_instruments(c('ieu-a-2', 'ieu-a-7'))
@@ -18,64 +23,54 @@ context("add metadata")
 load(system.file("extdata", "test_add_metadata.RData", package="TwoSampleMR"))
 
 test_that("exposure data 1", {
-  skip_on_ci()
 	d1 <- d1 %>% add_metadata()
 	expect_true("units.exposure" %in% names(d1))
 })
 
 test_that("exposure data 2", {
-  skip_on_ci()
 	d2 <- d2 %>% add_metadata()
 	expect_true("units.exposure" %in% names(d2))
 })
 
 test_that("outcome data 1", {
-  skip_on_ci()
 	d3 <- d3 %>% add_metadata()
 	expect_true("units.outcome" %in% names(d3))
 })
 
 test_that("outcome data 2", {
-  skip_on_ci()
 	d4 <- d4 %>% add_metadata()
 	expect_true("units.outcome" %in% names(d4))
 })
 
 test_that("dat 2", {
-  skip_on_ci()
 	d5 <- d5 %>% add_metadata()
 	expect_true("units.outcome" %in% names(d5) & "units.exposure" %in% names(d5))
 })
 
 test_that("no id1", {
-  skip_on_ci()
 	d6$id.exposure <- "not a real id"
 	d6 <- add_metadata(d6)
 	expect_true(!"units.exposure" %in% names(d6))
 })
 
 test_that("no id2", {
-  skip_on_ci()
 	d7$id.outcome <- "not a real id"
 	d7 <- add_metadata(d7)
 	expect_true(!"units.outcome" %in% names(d7))
 })
 
 test_that("ukb-d", {
-  skip_on_ci()
 	d8 <- add_metadata(d8)
 	expect_true("units.outcome" %in% names(d8))
 })
 
 test_that("bbj-a-1", {
-  skip_on_ci()
 	d9 <- d9 %>% add_metadata()
 	expect_true("samplesize.exposure" %in% names(d9))
 	expect_true(all(!is.na(d9$samplesize.exposure)))
 })
 
 test_that("ieu-b-109", {
-  skip_on_ci()
 	d10 <- d10 %>% add_metadata()
 	expect_true("samplesize.exposure" %in% names(d10))
 	expect_true(all(!is.na(d10$samplesize.exposure)))

From aa1cd257a631f11142120037ae336c8643c28949 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 21:13:29 +0100
Subject: [PATCH 14/48] Add additional skips

---
 tests/testthat/test_instruments.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/testthat/test_instruments.R b/tests/testthat/test_instruments.R
index 27c5cd13..dc098e90 100644
--- a/tests/testthat/test_instruments.R
+++ b/tests/testthat/test_instruments.R
@@ -2,6 +2,9 @@ context("Instruments")
 
 test_that("server and mrinstruments", {
 
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
+  skip_on_cran()
   skip_on_ci()
   
 	# no no

From deb737abdb5ce6394026c78df92143113bc8b439 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 21:20:32 +0100
Subject: [PATCH 15/48] Move skips to top of file

---
 tests/testthat/test_ld.R | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/tests/testthat/test_ld.R b/tests/testthat/test_ld.R
index caa7eaca..e59501e5 100644
--- a/tests/testthat/test_ld.R
+++ b/tests/testthat/test_ld.R
@@ -1,16 +1,17 @@
 context("ld")
 
+skip_if_offline()
+skip_if_offline(host = "api.opengwas.io")
+skip_on_cran()
+skip_on_ci()
+
 test_that("extract some data", {
-  skip_on_cran()
-  skip_on_ci()
   a <- extract_instruments(2, clump=FALSE)
   if(length(a) == 0) skip("Server issues")
   out <- clump_data(a)
 })
 
 test_that("clump", {
-	skip_on_ci()
-	skip_on_cran()
 	expect_equal(ncol(a), ncol(out))
 	expect_true(nrow(a) > nrow(out))
 	expect_true(nrow(out) > 0)
@@ -18,8 +19,7 @@ test_that("clump", {
 
 
 test_that("matrix", {
-	skip_on_ci()
-	skip_on_cran()
+  skip_if_not(exists('out'), "out not created in test above")
 	b <- ld_matrix(out$SNP)
 	expect_equal(nrow(b), nrow(out))
 	expect_equal(ncol(b), nrow(out))
@@ -27,16 +27,13 @@ test_that("matrix", {
 
 
 test_that("clump multiple", {
-	skip_on_ci()
-	skip_on_cran()
 	a <- extract_instruments(c("ieu-a-2", "ieu-a-1001"), clump=FALSE)
 	out <- clump_data(a)
 	expect_equal(length(unique(a$id.exposure)), length(unique(out$id.exposure)))
 })
 
 test_that("clump local", {
-	skip_on_ci()
-	skip_on_cran()
+  skip_if_not(exists('a'), "a not created in test above")
 	skip_if_not(file.exists("/Users/gh13047/repo/opengwas-api-internal/opengwas-api/app/ld_files/EUR.bim"))
 	aclump <- clump_data(a, bfile="/Users/gh13047/repo/opengwas-api-internal/opengwas-api/app/ld_files/EUR", plink_bin="plink")
 })

From 5d6c50511ae44bc6dd0c21d43819a1e03c79ff4c Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 21:20:47 +0100
Subject: [PATCH 16/48] Add two skips to test

---
 tests/testthat/test_ld.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/testthat/test_ld.R b/tests/testthat/test_ld.R
index e59501e5..99131501 100644
--- a/tests/testthat/test_ld.R
+++ b/tests/testthat/test_ld.R
@@ -12,6 +12,8 @@ test_that("extract some data", {
 })
 
 test_that("clump", {
+  skip_if_not(exists('a'), "a not created in test above")
+  skip_if_not(exists('out'), "out not created in test above")
 	expect_equal(ncol(a), ncol(out))
 	expect_true(nrow(a) > nrow(out))
 	expect_true(nrow(out) > 0)

From 25350e059f77d39b618fea6cae3d5f0c53e7e40c Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 21:24:13 +0100
Subject: [PATCH 17/48] Remove empty test

---
 tests/testthat/test_ld.R | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/tests/testthat/test_ld.R b/tests/testthat/test_ld.R
index 99131501..82256c82 100644
--- a/tests/testthat/test_ld.R
+++ b/tests/testthat/test_ld.R
@@ -5,11 +5,10 @@ skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()
 skip_on_ci()
 
-test_that("extract some data", {
-  a <- extract_instruments(2, clump=FALSE)
-  if(length(a) == 0) skip("Server issues")
-  out <- clump_data(a)
-})
+# extract some data
+a <- extract_instruments(2, clump=FALSE)
+if(length(a) == 0) skip("Server issues")
+out <- clump_data(a)
 
 test_that("clump", {
   skip_if_not(exists('a'), "a not created in test above")

From 4c106c123e9aac8d5065c2d2d5a11dee097be963 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 21:26:17 +0100
Subject: [PATCH 18/48] Add offline skips

---
 tests/testthat/test_mvmr_local.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/testthat/test_mvmr_local.R b/tests/testthat/test_mvmr_local.R
index 158d51ec..084559ef 100644
--- a/tests/testthat/test_mvmr_local.R
+++ b/tests/testthat/test_mvmr_local.R
@@ -10,6 +10,8 @@ context("mvmr local")
 load(system.file("extdata", "test_add_mvmr_local.RData", package="TwoSampleMR"))
 
 test_that("mv exposure local", {
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
 	skip_on_ci()
 	skip_on_cran()
     f1 <- tempfile()

From 9afa1e1d37037104b032f7c9b23713705b8985f2 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 21:28:16 +0100
Subject: [PATCH 19/48] Move skips to top of file

---
 tests/testthat/test_mvmr.R | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/tests/testthat/test_mvmr.R b/tests/testthat/test_mvmr.R
index 4025fe25..69b6c3fa 100644
--- a/tests/testthat/test_mvmr.R
+++ b/tests/testthat/test_mvmr.R
@@ -1,8 +1,11 @@
 context("mvmr")
 
+skip_on_ci()
+skip_on_cran()
+skip_if_offline()
+skip_if_offline(host = "api.opengwas.io")
+
 test_that("control", {
-	skip_on_ci()
-	skip_on_cran()
 	lipids <- mv_extract_exposures(c("ieu-a-299","ieu-a-300","ieu-a-302"))
 	chd <- extract_outcome_data(lipids$SNP, "ieu-a-7")
 	control <- mv_harmonise_data(lipids, chd)
@@ -18,8 +21,6 @@ test_that("control", {
 
 
 test_that("dat", {
-	skip_on_ci()
-	skip_on_cran()
 	a <- mv_extract_exposures(c("ukb-b-5238", "ieu-a-1001"))
 	b <- extract_outcome_data(a$SNP, "ieu-a-297")
 	dat <- mv_harmonise_data(a, b)
@@ -37,8 +38,6 @@ test_that("dat", {
 
 
 test_that("ordering", {
-	skip_on_ci()
-	skip_on_cran()
 	lipids1 <- mv_extract_exposures(c("ieu-a-299","ieu-a-300","ieu-a-302"))
 	chd1 <- extract_outcome_data(lipids1$SNP, "ieu-a-7")
 	control1 <- mv_harmonise_data(lipids1, chd1)

From 526a706a5a8f5840512888852db1e8d4df42525a Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 21:30:22 +0100
Subject: [PATCH 20/48] Add offline skips

---
 tests/testthat/test_otherformats.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/testthat/test_otherformats.R b/tests/testthat/test_otherformats.R
index e8fd11e5..28187514 100644
--- a/tests/testthat/test_otherformats.R
+++ b/tests/testthat/test_otherformats.R
@@ -14,6 +14,8 @@ test_that("MRInput", {
 test_that("MRInput with cor", {
   skip_on_cran()
   skip_on_ci()
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
 	expect_warning(w <- dat_to_MRInput(dat, get_correlations=TRUE)[[1]])
 	expect_true(nrow(w@correlation) == length(w@betaX))
 })

From 28cc0dbf7bc665a884be45bccb1c4e2b845ffdd3 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 21:31:19 +0100
Subject: [PATCH 21/48] Add two offline skips

---
 tests/testthat/test_outcomes.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/testthat/test_outcomes.R b/tests/testthat/test_outcomes.R
index d761acce..c7a095cf 100644
--- a/tests/testthat/test_outcomes.R
+++ b/tests/testthat/test_outcomes.R
@@ -2,6 +2,8 @@ context("outcome")
 
 test_that("outcomes", {
 
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
   skip_on_ci()
 

From 08e51cf05283026528945df30457525131ea0616 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sat, 29 Jun 2024 21:33:33 +0100
Subject: [PATCH 22/48] Add skips

---
 tests/testthat/test_rsq.r | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/tests/testthat/test_rsq.r b/tests/testthat/test_rsq.r
index 1fb1b39b..68417722 100644
--- a/tests/testthat/test_rsq.r
+++ b/tests/testthat/test_rsq.r
@@ -10,6 +10,9 @@ test_that("exposure data 1", {
 })
 
 test_that("exposure data 2", {
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
+  skip_on_cran()
   skip_on_ci()
   d <- extract_instruments(c('ieu-a-2', 'ieu-a-7'))
   if(inherits(d, "response")) skip("Server issues")
@@ -21,6 +24,9 @@ test_that("exposure data 2", {
 exposure <- exp_dat[1:5,]
 
 test_that("outcome data 1", {
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
+  skip_on_cran()
   skip_on_ci()
   d <- extract_outcome_data(exposure$SNP, 'ieu-a-2')
   if(inherits(d, "response")) skip("Server issues")
@@ -30,6 +36,9 @@ test_that("outcome data 1", {
 })
 
 test_that("outcome data 2", {
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
+  skip_on_cran()
   skip_on_ci()
   d <- extract_outcome_data(exposure$SNP, c('ieu-a-2', 'ieu-a-7'))
   if(inherits(d, "response")) skip("Server issues")
@@ -39,6 +48,9 @@ test_that("outcome data 2", {
 })
 
 test_that("dat 2", {
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
+  skip_on_cran()
   skip_on_ci()
   d <- make_dat(proxies=FALSE)
   if(inherits(d, "response")) skip("Server issues")
@@ -48,6 +60,9 @@ test_that("dat 2", {
 })
 
 test_that("dat ukb-d", {
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
+  skip_on_cran()
   skip_on_cran()
   skip_on_ci()
   d <- make_dat(exposure="ukb-d-30710_irnt", proxies=FALSE)
@@ -64,6 +79,9 @@ test_that("effective n", {
 })
 
 test_that("get_population_allele_frequency", {
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
+  skip_on_cran()
   skip_on_ci()
 	d <- extract_instruments("ieu-a-7")
 	if(inherits(d, "response")) skip("Server issues")
@@ -80,6 +98,8 @@ test_that("get_population_allele_frequency", {
 test_that("bbj-a-1", {
   skip_on_cran()
   skip_on_ci()
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
   d <- extract_instruments('bbj-a-1')
   if(inherits(d, "response")) skip("Server issues")
   d <- d %>% add_metadata() %>% add_rsq()
@@ -87,6 +107,9 @@ test_that("bbj-a-1", {
 })
 
 test_that("bsen vs pn", {
+  skip_if_offline()
+  skip_if_offline(host = "api.opengwas.io")
+  skip_on_cran()
   skip_on_ci()
   d <- extract_instruments("ieu-a-2")
   if(inherits(d, "response")) skip("Server issues")

From 0e1ac666a0ab689860548fc5e545a272025c1399 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 14:31:32 +0100
Subject: [PATCH 23/48] Catch server non-response with try()

---
 tests/testthat/test_instruments.R | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/tests/testthat/test_instruments.R b/tests/testthat/test_instruments.R
index dc098e90..c5803538 100644
--- a/tests/testthat/test_instruments.R
+++ b/tests/testthat/test_instruments.R
@@ -8,35 +8,43 @@ test_that("server and mrinstruments", {
   skip_on_ci()
   
 	# no no
-	exp_dat <- extract_instruments(outcomes=c("ieu-a-1032"))
+  exp_dat <- try(extract_instruments(outcomes=c("ieu-a-1032")))
+  if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 0)
 
 	# no yes
-	exp_dat <- extract_instruments(outcomes=c("ebi-a-GCST004634"))
+	exp_dat <- try(extract_instruments(outcomes=c("ebi-a-GCST004634")))
+	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 1)
 
 	# yes no
-	exp_dat <- extract_instruments(outcomes=c("ieu-a-2", "ieu-a-1032"))
+	exp_dat <- try(extract_instruments(outcomes=c("ieu-a-2", "ieu-a-1032")))
+	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 1)
 
 	# yes yes
-	exp_dat <- extract_instruments(outcomes=c("ieu-a-2", "ebi-a-GCST004634"))
+	exp_dat <- try(extract_instruments(outcomes=c("ieu-a-2", "ebi-a-GCST004634")))
+	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 2)
 
-	exp_dat <- extract_instruments(outcomes=c("ieu-a-1032", "ebi-a-GCST004634"))
+	exp_dat <- try(extract_instruments(outcomes=c("ieu-a-1032", "ebi-a-GCST004634")))
+	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 1)
 
-	exp_dat <- extract_instruments(outcomes=c(2,100,"ieu-a-1032",104,72,999))
+	exp_dat <- try(extract_instruments(outcomes=c(2,100,"ieu-a-1032",104,72,999)))
+	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 5)
 
-	exp_dat <- extract_instruments(outcomes=c(2,100,"ieu-a-1032",104,72,999, "ebi-a-GCST004634"))
+	exp_dat <- try(extract_instruments(outcomes=c(2,100,"ieu-a-1032",104,72,999, "ebi-a-GCST004634")))
+	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 6)
 })
 
 load(system.file("extdata", "test_commondata.RData", package="TwoSampleMR"))
 
 test_that("read data", {
-	# exp_dat <- extract_instruments("ieu-a-2")
+	exp_dat <- try(extract_instruments("ieu-a-2"))
+	if (class(exp_dat) == "try-error") skip("Server issues")
 	names(exp_dat) <- gsub(".exposure", "", names(exp_dat))
 	fn <- tempfile()
 	write.table(exp_dat, file=fn, row=FALSE, col=TRUE, qu=FALSE, sep="\t")

From ef7d8c062cfaf8912895c1deed3a76e7830192ed Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 14:33:21 +0100
Subject: [PATCH 24/48] Split into separate tests

---
 tests/testthat/test_instruments.R | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/tests/testthat/test_instruments.R b/tests/testthat/test_instruments.R
index c5803538..4bde502e 100644
--- a/tests/testthat/test_instruments.R
+++ b/tests/testthat/test_instruments.R
@@ -1,40 +1,52 @@
 context("Instruments")
 
-test_that("server and mrinstruments", {
+skip_if_offline()
+skip_if_offline(host = "api.opengwas.io")
+skip_on_cran()
+skip_on_ci()
 
-  skip_if_offline()
-  skip_if_offline(host = "api.opengwas.io")
-  skip_on_cran()
-  skip_on_ci()
-  
+test_that("server and mrinstruments 1", {
 	# no no
   exp_dat <- try(extract_instruments(outcomes=c("ieu-a-1032")))
   if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 0)
+})
+
 
+test_that("server and mrinstruments 2", {
 	# no yes
 	exp_dat <- try(extract_instruments(outcomes=c("ebi-a-GCST004634")))
 	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 1)
-
+})
+	
+test_that("server and mrinstruments 3", {
 	# yes no
 	exp_dat <- try(extract_instruments(outcomes=c("ieu-a-2", "ieu-a-1032")))
 	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 1)
+})
 
+test_that("server and mrinstruments 4", {
 	# yes yes
 	exp_dat <- try(extract_instruments(outcomes=c("ieu-a-2", "ebi-a-GCST004634")))
 	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 2)
+})
 
+test_that("server and mrinstruments 5", {
 	exp_dat <- try(extract_instruments(outcomes=c("ieu-a-1032", "ebi-a-GCST004634")))
 	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 1)
+})
 
+test_that("server and mrinstruments 6", {
 	exp_dat <- try(extract_instruments(outcomes=c(2,100,"ieu-a-1032",104,72,999)))
 	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 5)
+})
 
+test_that("server and mrinstruments 7", {
 	exp_dat <- try(extract_instruments(outcomes=c(2,100,"ieu-a-1032",104,72,999, "ebi-a-GCST004634")))
 	if (class(exp_dat) == "try-error") skip("Server issues")
 	expect_true(length(unique(exp_dat$id)) == 6)

From 347c9ccb1e04000ad735ffb6f79fba2946372c64 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 14:38:06 +0100
Subject: [PATCH 25/48] Add try() to catch server non-response

---
 tests/testthat/test_add_metadata.r | 30 ++++++++++++++++++++----------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/tests/testthat/test_add_metadata.r b/tests/testthat/test_add_metadata.r
index 4c30cce5..4207df4f 100644
--- a/tests/testthat/test_add_metadata.r
+++ b/tests/testthat/test_add_metadata.r
@@ -23,55 +23,65 @@ skip_on_ci()
 load(system.file("extdata", "test_add_metadata.RData", package="TwoSampleMR"))
 
 test_that("exposure data 1", {
-	d1 <- d1 %>% add_metadata()
+	d1 <- try(d1 %>% add_metadata())
+	if (class(d1) == "try-error") skip("Server issues")
 	expect_true("units.exposure" %in% names(d1))
 })
 
 test_that("exposure data 2", {
-	d2 <- d2 %>% add_metadata()
+	d2 <- try(d2 %>% add_metadata())
+	if (class(d2) == "try-error") skip("Server issues")
 	expect_true("units.exposure" %in% names(d2))
 })
 
 test_that("outcome data 1", {
-	d3 <- d3 %>% add_metadata()
+	d3 <- try(d3 %>% add_metadata())
+	if (class(d3) == "try-error") skip("Server issues")
 	expect_true("units.outcome" %in% names(d3))
 })
 
 test_that("outcome data 2", {
-	d4 <- d4 %>% add_metadata()
+	d4 <- try(d4 %>% add_metadata())
+	if (class(d4) == "try-error") skip("Server issues")
 	expect_true("units.outcome" %in% names(d4))
 })
 
 test_that("dat 2", {
-	d5 <- d5 %>% add_metadata()
+	d5 <- try(d5 %>% add_metadata())
+	if (class(d5) == "try-error") skip("Server issues")
 	expect_true("units.outcome" %in% names(d5) & "units.exposure" %in% names(d5))
 })
 
 test_that("no id1", {
 	d6$id.exposure <- "not a real id"
-	d6 <- add_metadata(d6)
+	d6 <- try(add_metadata(d6))
+	if (class(d6) == "try-error") skip("Server issues")
 	expect_true(!"units.exposure" %in% names(d6))
 })
 
 test_that("no id2", {
 	d7$id.outcome <- "not a real id"
-	d7 <- add_metadata(d7)
+	d7 <- try(add_metadata(d7))
+	if (class(d7) == "try-error") skip("Server issues")
 	expect_true(!"units.outcome" %in% names(d7))
 })
 
 test_that("ukb-d", {
-	d8 <- add_metadata(d8)
+	d8 <- try(add_metadata(d8))
+	if (class(d8) == "try-error") skip("Server issues")
 	expect_true("units.outcome" %in% names(d8))
 })
 
 test_that("bbj-a-1", {
-	d9 <- d9 %>% add_metadata()
+	d9 <- try(d9 %>% add_metadata())
+	if (class(d9) == "try-error") skip("Server issues")
 	expect_true("samplesize.exposure" %in% names(d9))
 	expect_true(all(!is.na(d9$samplesize.exposure)))
 })
 
 test_that("ieu-b-109", {
-	d10 <- d10 %>% add_metadata()
+	d10 <- try(d10 %>% add_metadata())
+	if (class(d10) == "try-error") skip("Server issues")
 	expect_true("samplesize.exposure" %in% names(d10))
 	expect_true(all(!is.na(d10$samplesize.exposure)))
 })

From 3c4962afc9456f1adaf81e0983d0d19cfbaf5e7f Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 14:49:10 +0100
Subject: [PATCH 26/48] Add try() to catch server non-response

---
 tests/testthat/test_ld.R | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/tests/testthat/test_ld.R b/tests/testthat/test_ld.R
index 82256c82..fb386c1d 100644
--- a/tests/testthat/test_ld.R
+++ b/tests/testthat/test_ld.R
@@ -6,9 +6,11 @@ skip_on_cran()
 skip_on_ci()
 
 # extract some data
-a <- extract_instruments(2, clump=FALSE)
-if(length(a) == 0) skip("Server issues")
-out <- clump_data(a)
+a <- try(extract_instruments("ieu-a-2", clump=FALSE))
+if (class(a) == "try-error") skip("Server issues")
+out <- try(clump_data(a))
+if (class(out) == "try-error") skip("Server issues")
+
 
 test_that("clump", {
   skip_if_not(exists('a'), "a not created in test above")
@@ -21,14 +23,16 @@ test_that("clump", {
 
 test_that("matrix", {
   skip_if_not(exists('out'), "out not created in test above")
-	b <- ld_matrix(out$SNP)
+	b <- try(ld_matrix(out$SNP))
+	if (inherits(b, "try-error")) skip("Server issues")
 	expect_equal(nrow(b), nrow(out))
 	expect_equal(ncol(b), nrow(out))
 })
 
 
 test_that("clump multiple", {
-	a <- extract_instruments(c("ieu-a-2", "ieu-a-1001"), clump=FALSE)
+	a <- try(extract_instruments(c("ieu-a-2", "ieu-a-1001"), clump=FALSE))
+	if (class(a) == "try-error") skip("Server issues")
 	out <- clump_data(a)
 	expect_equal(length(unique(a$id.exposure)), length(unique(out$id.exposure)))
 })

From bc0e31388770da75ffcc03fad0b11e9832a81b18 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 14:51:23 +0100
Subject: [PATCH 27/48] Add try() to catch server non-response

---
 tests/testthat/test_mvmr_local.R | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/tests/testthat/test_mvmr_local.R b/tests/testthat/test_mvmr_local.R
index 084559ef..4c2a636c 100644
--- a/tests/testthat/test_mvmr_local.R
+++ b/tests/testthat/test_mvmr_local.R
@@ -19,7 +19,7 @@ test_that("mv exposure local", {
     write.table(a1, file=f1, row.names = FALSE, col.names = TRUE, quote = FALSE, sep="\t")
     write.table(a2, file=f2, row.names = FALSE, col.names = TRUE, quote = FALSE, sep="\t")
 
-    exposure_dat <- mv_extract_exposures_local(
+    exposure_dat <- try(mv_extract_exposures_local(
         c(f1, f2),
         sep = "\t",
         snp_col=c("rsid"),
@@ -28,9 +28,11 @@ test_that("mv exposure local", {
         effect_allele_col=c("ea"),
         other_allele_col=c("nea"),
         pval_col=c("p")
-    )
+    ))
+    if (inherits(exposure_dat, "try-error")) skip("Server issues")
+    expect_true(nrow(exposure_dat) > 100)
 
-    exposure_dat2 <- mv_extract_exposures_local(
+    exposure_dat2 <- try(mv_extract_exposures_local(
         list(a1, a2),
         sep = "\t",
         snp_col=c("rsid"),
@@ -39,8 +41,7 @@ test_that("mv exposure local", {
         effect_allele_col=c("ea"),
         other_allele_col=c("nea"),
         pval_col=c("p")
-    )
-
-    expect_true(nrow(exposure_dat) > 100)
+    ))
+    if (inherits(exposure_dat2, "try-error")) skip("Server issues")
     expect_true(all.equal(exposure_dat, exposure_dat2))
 })

From 763a1652877c8d3dee3f541977d4e71f219ba13a Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 14:54:23 +0100
Subject: [PATCH 28/48] Split into separate tests

---
 tests/testthat/test_mvmr.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test_mvmr.R b/tests/testthat/test_mvmr.R
index 69b6c3fa..2128d953 100644
--- a/tests/testthat/test_mvmr.R
+++ b/tests/testthat/test_mvmr.R
@@ -37,12 +37,14 @@ test_that("dat", {
 })
 
 
-test_that("ordering", {
+test_that("ordering 1", {
 	lipids1 <- mv_extract_exposures(c("ieu-a-299","ieu-a-300","ieu-a-302"))
 	chd1 <- extract_outcome_data(lipids1$SNP, "ieu-a-7")
 	control1 <- mv_harmonise_data(lipids1, chd1)
 	expect_output(print(mv_multiple(control1)))
+})
 
+test_that("ordering 2", {
 	lipids2 <- mv_extract_exposures(c("ieu-a-302","ieu-a-300","ieu-a-299"))
 	chd2 <- extract_outcome_data(lipids2$SNP, "ieu-a-7")
 	control2 <- mv_harmonise_data(lipids2, chd2)

From 3a832dada43d23253c24aa116192886442caac61 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 14:57:17 +0100
Subject: [PATCH 29/48] Add try() to catch server non-response

---
 tests/testthat/test_mvmr.R | 36 ++++++++++++++++++++++++------------
 1 file changed, 24 insertions(+), 12 deletions(-)

diff --git a/tests/testthat/test_mvmr.R b/tests/testthat/test_mvmr.R
index 2128d953..dbc6658c 100644
--- a/tests/testthat/test_mvmr.R
+++ b/tests/testthat/test_mvmr.R
@@ -6,9 +6,12 @@ skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 
 test_that("control", {
-	lipids <- mv_extract_exposures(c("ieu-a-299","ieu-a-300","ieu-a-302"))
-	chd <- extract_outcome_data(lipids$SNP, "ieu-a-7")
-	control <- mv_harmonise_data(lipids, chd)
+	lipids <- try(mv_extract_exposures(c("ieu-a-299","ieu-a-300","ieu-a-302")))
+	if (inherits(lipids, "try-error")) skip("Server issues")
+	chd <- try(extract_outcome_data(lipids$SNP, "ieu-a-7"))
+	if (inherits(chd, "try-error")) skip("Server issues")
+	control <- try(mv_harmonise_data(lipids, chd))
+	if (inherits(control, "try-error")) skip("Server issues")
 	expect_output(print(mv_residual(control, intercept=TRUE, instrument_specific=TRUE)))
 	expect_output(print(mv_residual(control, intercept=FALSE, instrument_specific=TRUE)))
 	expect_output(print(mv_residual(control, intercept=TRUE, instrument_specific=FALSE)))
@@ -21,9 +24,12 @@ test_that("control", {
 
 
 test_that("dat", {
-	a <- mv_extract_exposures(c("ukb-b-5238", "ieu-a-1001"))
-	b <- extract_outcome_data(a$SNP, "ieu-a-297")
-	dat <- mv_harmonise_data(a, b)
+	a <- try(mv_extract_exposures(c("ukb-b-5238", "ieu-a-1001")))
+	if (inherits(a, "try-error")) skip("Server issues")
+	b <- try(extract_outcome_data(a$SNP, "ieu-a-297"))
+	if (inherits(b, "try-error")) skip("Server issues")
+	dat <- try(mv_harmonise_data(a, b))
+	if (inherits(dat, "try-error")) skip("Server issues")
 	expect_output(print(mv_residual(dat, intercept=TRUE, instrument_specific=TRUE)))
 	expect_output(print(mv_residual(dat, intercept=FALSE, instrument_specific=TRUE)))
 	expect_output(print(mv_residual(dat, intercept=TRUE, instrument_specific=FALSE)))
@@ -38,15 +44,21 @@ test_that("dat", {
 
 
 test_that("ordering 1", {
-	lipids1 <- mv_extract_exposures(c("ieu-a-299","ieu-a-300","ieu-a-302"))
-	chd1 <- extract_outcome_data(lipids1$SNP, "ieu-a-7")
-	control1 <- mv_harmonise_data(lipids1, chd1)
+	lipids1 <- try(mv_extract_exposures(c("ieu-a-299","ieu-a-300","ieu-a-302")))
+	if (inherits(lipids1, "try-error")) skip("Server issues")
+	chd1 <- try(extract_outcome_data(lipids1$SNP, "ieu-a-7"))
+	if (inherits(chd1, "try-error")) skip("Server issues")
+	control1 <- try(mv_harmonise_data(lipids1, chd1))
+	if (inherits(control1, "try-error")) skip("Server issues")
 	expect_output(print(mv_multiple(control1)))
 })
 
 test_that("ordering 2", {
-	lipids2 <- mv_extract_exposures(c("ieu-a-302","ieu-a-300","ieu-a-299"))
-	chd2 <- extract_outcome_data(lipids2$SNP, "ieu-a-7")
-	control2 <- mv_harmonise_data(lipids2, chd2)
+	lipids2 <- try(mv_extract_exposures(c("ieu-a-302","ieu-a-300","ieu-a-299")))
+	if (inherits(lipids2, "try-error")) skip("Server issues")
+	chd2 <- try(extract_outcome_data(lipids2$SNP, "ieu-a-7"))
+	if (inherits(chd2, "try-error")) skip("Server issues")
+	control2 <- try(mv_harmonise_data(lipids2, chd2))
+	if (inherits(control2, "try-error")) skip("Server issues")
 	expect_output(print(mv_multiple(control2)))
 })

From 4206d2c8cf668ebbe1d40478304afd53a18c2d75 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:05:11 +0100
Subject: [PATCH 30/48] Split into separate tests and use try()

---
 tests/testthat/test_outcomes.R | 43 ++++++++++++++++++++--------------
 1 file changed, 26 insertions(+), 17 deletions(-)

diff --git a/tests/testthat/test_outcomes.R b/tests/testthat/test_outcomes.R
index c7a095cf..da9d672c 100644
--- a/tests/testthat/test_outcomes.R
+++ b/tests/testthat/test_outcomes.R
@@ -1,36 +1,45 @@
 context("outcome")
 
-test_that("outcomes", {
+skip_if_offline()
+skip_if_offline(host = "api.opengwas.io")
+skip_on_cran()
+skip_on_ci()
 
-  skip_if_offline()
-  skip_if_offline(host = "api.opengwas.io")
-  skip_on_cran()
-  skip_on_ci()
+a <- try(extract_instruments("ieu-a-7"))
+if(inherits(a, "try-error")) skip("Server issues")
 
-	a <- extract_instruments("ieu-a-7")
-	if(inherits(a, "response")) skip("Server issues")
-	b <- extract_outcome_data(a$SNP, "ieu-a-2", proxies=FALSE)
-	if(inherits(b, "response")) skip("Server issues")
+test_that("outcomes 1", {
+	b <- try(extract_outcome_data(a$SNP, "ieu-a-2", proxies=FALSE))
+	if(inherits(b, "try-error")) skip("Server issues")
 	expect_true(nrow(b) < 30 & nrow(b) > 15)
+})
 
-	b <- extract_outcome_data(a$SNP, "ieu-a-2", proxies=TRUE)
-	if(inherits(b, "response")) skip("Server issues")
+test_that("outcomes 2", {
+	b <- try(extract_outcome_data(a$SNP, "ieu-a-2", proxies=TRUE))
+	if(inherits(b, "try-error")) skip("Server issues")
 	expect_true(nrow(b) > 30 & nrow(b) < nrow(a))
+})
 
-	b <- extract_outcome_data(a$SNP, c("ieu-a-2", "a"), proxies=FALSE)
-	if(inherits(b, "response")) skip("Server issues")
+test_that("outcomes 3", {
+	b <- try(extract_outcome_data(a$SNP, c("ieu-a-2", "a"), proxies=FALSE))
+	if(inherits(b, "try-error")) skip("Server issues")
 	expect_true(nrow(b) < 30 & nrow(b) > 15)
+})
 
+test_that("outcomes 4", {
 	b <- extract_outcome_data(a$SNP, c("ieu-a-2", "a"), proxies=TRUE)
-	if(inherits(b, "response")) skip("Server issues")
+	if(inherits(b, "try-error")) skip("Server issues")
 	expect_true(nrow(b) > 30 & nrow(b) < nrow(a))
+})
 
+test_that("outcomes 5", {
 	b <- extract_outcome_data(a$SNP, c("ieu-a-2", "ieu-a-7"), proxies=FALSE)
-	if(inherits(b, "response")) skip("Server issues")
+	if(inherits(b, "try-error")) skip("Server issues")
 	expect_true(nrow(b) > 60)
+})
 
+test_that("outcomes 6", {
 	b <- extract_outcome_data(a$SNP, c("ieu-a-2", "ieu-a-7"), proxies=TRUE)
-	if(inherits(b, "response")) skip("Server issues")
+	if(inherits(b, "try-error")) skip("Server issues")
 	expect_true(nrow(b) > 70)
-
 })

From c6286c101925d1bc44934d93cded63e850e75396 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:12:01 +0100
Subject: [PATCH 31/48] Use try() to catch server non-response

---
 tests/testthat/test_rsq.r | 38 ++++++++++++++++++++------------------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/tests/testthat/test_rsq.r b/tests/testthat/test_rsq.r
index 68417722..407cf201 100644
--- a/tests/testthat/test_rsq.r
+++ b/tests/testthat/test_rsq.r
@@ -14,8 +14,8 @@ test_that("exposure data 2", {
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
   skip_on_ci()
-  d <- extract_instruments(c('ieu-a-2', 'ieu-a-7'))
-  if(inherits(d, "response")) skip("Server issues")
+  d <- try(extract_instruments(c('ieu-a-2', 'ieu-a-7')))
+  if(inherits(d, "try-error")) skip("Server issues")
   d <- d %>% add_rsq()
 	expect_true("rsq.exposure" %in% names(d))
 	expect_true("effective_n.exposure" %in% names(d))
@@ -28,8 +28,8 @@ test_that("outcome data 1", {
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
   skip_on_ci()
-  d <- extract_outcome_data(exposure$SNP, 'ieu-a-2')
-  if(inherits(d, "response")) skip("Server issues")
+  d <- try(extract_outcome_data(exposure$SNP, 'ieu-a-2'))
+  if(inherits(d, "try-error")) skip("Server issues")
   d <- d %>% add_rsq()
 	expect_true("rsq.outcome" %in% names(d))
 	expect_true("effective_n.outcome" %in% names(d))
@@ -40,8 +40,8 @@ test_that("outcome data 2", {
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
   skip_on_ci()
-  d <- extract_outcome_data(exposure$SNP, c('ieu-a-2', 'ieu-a-7'))
-  if(inherits(d, "response")) skip("Server issues")
+  d <- try(extract_outcome_data(exposure$SNP, c('ieu-a-2', 'ieu-a-7')))
+  if(inherits(d, "try-error")) skip("Server issues")
   d <- d %>% add_rsq()
 	expect_true("rsq.outcome" %in% names(d))
 	expect_true("effective_n.outcome" %in% names(d))
@@ -52,8 +52,8 @@ test_that("dat 2", {
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
   skip_on_ci()
-  d <- make_dat(proxies=FALSE)
-  if(inherits(d, "response")) skip("Server issues")
+  d <- try(make_dat(proxies=FALSE))
+  if(inherits(d, "try-error")) skip("Server issues")
   d <- d %>% add_rsq()
 	expect_true("rsq.outcome" %in% names(d) & "rsq.exposure" %in% names(d))
 	expect_true("effective_n.outcome" %in% names(d) & "effective_n.exposure" %in% names(d))
@@ -65,8 +65,8 @@ test_that("dat ukb-d", {
   skip_on_cran()
   skip_on_cran()
   skip_on_ci()
-  d <- make_dat(exposure="ukb-d-30710_irnt", proxies=FALSE)
-  if(inherits(d, "response")) skip("Server issues")
+  d <- try(make_dat(exposure="ukb-d-30710_irnt", proxies=FALSE))
+  if(inherits(d, "try-error")) skip("Server issues")
   d <- d %>% add_rsq()
 	expect_true("rsq.outcome" %in% names(d) & "rsq.exposure" %in% names(d))
 })
@@ -83,9 +83,10 @@ test_that("get_population_allele_frequency", {
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
   skip_on_ci()
-	d <- extract_instruments("ieu-a-7")
-	if(inherits(d, "response")) skip("Server issues")
-	d <- add_metadata(d)
+	d <- try(extract_instruments("ieu-a-7"))
+	if(inherits(d, "try-error")) skip("Server issues")
+	d <- try(add_metadata(d))
+	if(inherits(d, "try-error")) skip("Server issues")
 	d$eaf.exposure.controls <- get_population_allele_frequency(
 		af = d$eaf.exposure,
 		prop = d$ncase.exposure / (d$ncase.exposure + d$ncontrol.exposure),
@@ -100,9 +101,10 @@ test_that("bbj-a-1", {
   skip_on_ci()
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
-  d <- extract_instruments('bbj-a-1')
-  if(inherits(d, "response")) skip("Server issues")
-  d <- d %>% add_metadata() %>% add_rsq()
+  d <- try(extract_instruments('bbj-a-1'))
+  if(inherits(d, "try-error")) skip("Server issues")
+  d <- try(d %>% add_metadata() %>% add_rsq())
+  if(inherits(d, "try-error")) skip("Server issues")
 	expect_true(all(!is.na(d$rsq.exposure)))
 })
 
@@ -111,8 +113,8 @@ test_that("bsen vs pn", {
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
   skip_on_ci()
-  d <- extract_instruments("ieu-a-2")
-  if(inherits(d, "response")) skip("Server issues")
+  d <- try(extract_instruments("ieu-a-2"))
+  if(inherits(d, "try-error")) skip("Server issues")
 	r1 <- get_r_from_bsen(d$beta.exposure, d$se.exposure, d$samplesize.exposure)
 	r2 <- get_r_from_pn(d$pval.exposure, d$samplesize.exposure)
 	expect_true(cor(abs(r1), r2) > 0.99)

From 58689aca1f3099a2c937c5af764e59ac959ad004 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:12:26 +0100
Subject: [PATCH 32/48] Delete whitespace

---
 tests/testthat/test_singlesnp.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/testthat/test_singlesnp.R b/tests/testthat/test_singlesnp.R
index 8ce54e3a..bc29c7f1 100644
--- a/tests/testthat/test_singlesnp.R
+++ b/tests/testthat/test_singlesnp.R
@@ -3,13 +3,11 @@ context("singlesnp")
 # dat <- make_dat("ieu-a-2", "ieu-a-7")
 load(system.file("extdata", "test_commondata.RData", package="TwoSampleMR"))
 
-
 test_that("singlesnp", {
 	w <- mr_singlesnp(dat)
 	expect_true(nrow(w) == sum(dat$mr_keep) + 2)
 })
 
-
 test_that("singlesnp_plot", {
 	w <- mr_singlesnp(dat)
 	p <- mr_forest_plot(w)

From 605f0b4c89b1e3aeff96caa3c6839e6778a4ea49 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:12:50 +0100
Subject: [PATCH 33/48] Delete blank lines

---
 tests/testthat/test_steiger.R | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/tests/testthat/test_steiger.R b/tests/testthat/test_steiger.R
index 7740e952..e75e3cfe 100644
--- a/tests/testthat/test_steiger.R
+++ b/tests/testthat/test_steiger.R
@@ -3,20 +3,17 @@ context("steiger")
 # w <- make_dat(2, 7)
 load(system.file("extdata", "test_commondata.RData", package="TwoSampleMR"))
 
-
 test_that("directionality", {
 	o <- directionality_test(dat)
 	expect_true(nrow(o) == 1)
 })
 
-
 test_that("directionality cc", {
 	dat$r.outcome <- get_r_from_lor(dat$beta.outcome, dat$eaf.outcome, dat$samplesize.outcome/2, dat$samplesize.outcome/2, 0.1)
 	o <- directionality_test(dat)
 	expect_true(nrow(o) == 1)
 })
 
-
 test_that("steiger filtering", {
 	expect_warning(dat <- steiger_filtering(dat))
 	expect_true("steiger_pval" %in% names(dat))

From dbe176af3bf3c053d8a9c45a31d35a7f2ab3d0c3 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:14:02 +0100
Subject: [PATCH 34/48] Delete blank line

---
 tests/testthat/test_eve.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test_eve.R b/tests/testthat/test_eve.R
index 92b213f6..9f0623c2 100644
--- a/tests/testthat/test_eve.R
+++ b/tests/testthat/test_eve.R
@@ -3,7 +3,6 @@ context("eve")
 # dat <- make_dat("ieu-a-2", "ieu-a-7") %>% add_metadata()
 load(system.file("extdata", "test_commondata.RData", package="TwoSampleMR"))
 
-
 test_that("wrapper", {
   skip_if_not_installed("car")
 	expect_warning(w <- mr_wrapper(dat))

From 7f87268306b3ecb357e2047413cc0fd7a2318f3c Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:14:09 +0100
Subject: [PATCH 35/48] Delete blank lines

---
 tests/testthat/test_harmonise_edge_cases.R | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/tests/testthat/test_harmonise_edge_cases.R b/tests/testthat/test_harmonise_edge_cases.R
index 987ccf63..e2c7288f 100644
--- a/tests/testthat/test_harmonise_edge_cases.R
+++ b/tests/testthat/test_harmonise_edge_cases.R
@@ -6,7 +6,6 @@ set.seed(1)
 old <- options(stringsAsFactors = FALSE)
 on.exit(options(old), add = TRUE)
 
-
 df <- data.frame(
     "SNP" = c("9_69001927_C_T", "9_69459263_A_G", "9_69508544_G_A"),
     "effect_allele" = c("T", "G", "A"),
@@ -47,7 +46,6 @@ df_out <- format_data(
     samplesize_col = "n"
 )
 
-
 test_that("harmonise_data works when exposure and outcome df are 1 row.", {
     for (i in seq(1,3)) {
         result <- harmonise_data(
@@ -59,7 +57,6 @@ test_that("harmonise_data works when exposure and outcome df are 1 row.", {
     }
 })
 
-
 test_that("harmonise_data works when there are no matching SNPs.", {
     for (i in seq(1,3)) {
         df_out$SNP <- paste(df_out$SNP, "foo", sep = "_")

From 119039d08177885c18a17ee0594c24460ca1ceec Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:16:00 +0100
Subject: [PATCH 36/48] Amend 2 to "ieu-a-2"

---
 R/moe.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/moe.R b/R/moe.R
index 0aeaff11..89dd07d0 100644
--- a/R/moe.R
+++ b/R/moe.R
@@ -171,7 +171,7 @@ get_rsq <- function(dat)
 #' \dontrun{
 #' # Example of body mass index on coronary heart disease
 #' # Extract and harmonise data
-#' a <- extract_instruments(2)
+#' a <- extract_instruments("ieu-a-2")
 #' b <- extract_outcome_data(a$SNP, 7)
 #' dat <- harmonise_data(a,b)
 #' 

From feb271f0d8240d82213f4a24511bac153a28e180 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:16:06 +0100
Subject: [PATCH 37/48] Formatting

---
 R/moe.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/moe.R b/R/moe.R
index 89dd07d0..b723436f 100644
--- a/R/moe.R
+++ b/R/moe.R
@@ -173,7 +173,7 @@ get_rsq <- function(dat)
 #' # Extract and harmonise data
 #' a <- extract_instruments("ieu-a-2")
 #' b <- extract_outcome_data(a$SNP, 7)
-#' dat <- harmonise_data(a,b)
+#' dat <- harmonise_data(a, b)
 #' 
 #' # Apply all MR methods
 #' r <- mr_wrapper(dat)

From 51500652e80b17e8e4105453efa395311998fe7b Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:16:26 +0100
Subject: [PATCH 38/48] devtools::document()

---
 man/mr_moe.Rd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/mr_moe.Rd b/man/mr_moe.Rd
index bf8348e0..dcd79ac9 100644
--- a/man/mr_moe.Rd
+++ b/man/mr_moe.Rd
@@ -32,9 +32,9 @@ Note that the mixture of experts has only been trained on datasets with at least
 \dontrun{
 # Example of body mass index on coronary heart disease
 # Extract and harmonise data
-a <- extract_instruments(2)
+a <- extract_instruments("ieu-a-2")
 b <- extract_outcome_data(a$SNP, 7)
-dat <- harmonise_data(a,b)
+dat <- harmonise_data(a, b)
 
 # Apply all MR methods
 r <- mr_wrapper(dat)

From f387eae6cbeefa13134d5b759d4752d122f58467 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:17:38 +0100
Subject: [PATCH 39/48] Amend old names

---
 tests/testthat/test_plots.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test_plots.R b/tests/testthat/test_plots.R
index f050778c..c83c15fc 100644
--- a/tests/testthat/test_plots.R
+++ b/tests/testthat/test_plots.R
@@ -3,7 +3,7 @@ context("plots")
 load(system.file("extdata", "test_commondata.RData", package="TwoSampleMR"))
 
 test_that("scatter plot", {
-	# dat <- make_dat(2,7)
+	# dat <- make_dat("ieu-a-2", "ieu-a-7")
 	m <- mr(dat, method_list="mr_ivw")
 	p <- mr_scatter_plot(m, dat)
 	expect_true(is.list(p))

From 63cb3df854b1aad3936e8ef2931effd8880062fa Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:18:41 +0100
Subject: [PATCH 40/48] Amend old names

---
 tests/testthat/test_steiger.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test_steiger.R b/tests/testthat/test_steiger.R
index e75e3cfe..582dabf4 100644
--- a/tests/testthat/test_steiger.R
+++ b/tests/testthat/test_steiger.R
@@ -1,6 +1,6 @@
 context("steiger")
 
-# w <- make_dat(2, 7)
+# dat <- make_dat("ieu-a-2", "ieu-a-7")
 load(system.file("extdata", "test_commondata.RData", package="TwoSampleMR"))
 
 test_that("directionality", {

From d397b7229cf56327a403dbaa14eea7e0fca0e92e Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:21:34 +0100
Subject: [PATCH 41/48] Add tests bullet

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 2db51dc9..add27267 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,7 @@
 
 * Bumped version of **roxygen2** for creating package documentation
 * Update the earliest version of R in the `R CMD check` GitHub Actions workflow to be 4.3.2. This is because the **meta** dependency depends on **lme4**, and the recent 1.1-35.4 release of **lme4** requires **Matrix** 1.6-2 which was released a few days after R 4.3.2.
+* Made package tests more robust to non-response from the OpenGWAS API
 
 # TwoSampleMR v0.6.4
 

From d86623b71f7a9a288ebca69a20f8a5e6eb360fd2 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:21:55 +0100
Subject: [PATCH 42/48] Add release date

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index add27267..01fd5e3f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,6 @@
 # TwoSampleMR v0.6.5
 
-(Release date: 2024-##-##)
+(Release date: 2024-06-30)
 
 * Bumped version of **roxygen2** for creating package documentation
 * Update the earliest version of R in the `R CMD check` GitHub Actions workflow to be 4.3.2. This is because the **meta** dependency depends on **lme4**, and the recent 1.1-35.4 release of **lme4** requires **Matrix** 1.6-2 which was released a few days after R 4.3.2.

From 2739d3e8bcc68e6d0d51df320b241eab05a4645c Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:33:32 +0100
Subject: [PATCH 43/48] Delete blank line

---
 NEWS.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 01fd5e3f..eb289b4f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -11,7 +11,6 @@
 (Release date: 2024-06-05)
 
 * Update installation instructions in README.md
-
 * Fixed a bug in which the wrong indels recoding function was called (thanks @ruochiz)
 
 # TwoSampleMR v0.6.3

From c9de9c32756863584a3dc70bed3d01595e7703fa Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:46:43 +0100
Subject: [PATCH 44/48] Update test-coverage.yaml

---
 .github/workflows/test-coverage.yaml | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 8b5140c2..ca096091 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -24,7 +24,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Create and populate .Renviron file
@@ -34,15 +34,22 @@ jobs:
 
       - name: Test coverage
         run: |
-          token <- Sys.getenv("CODECOV_TOKEN", "")
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
-            token = if (token != "") token
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |

From 7408edd4e3d1713576d7f6ab53389fdced4138b3 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 15:54:25 +0100
Subject: [PATCH 45/48] Delete skip_on_ci()

---
 tests/testthat/test_add_metadata.r | 1 -
 tests/testthat/test_instruments.R  | 1 -
 tests/testthat/test_ld.R           | 1 -
 tests/testthat/test_mvmr.R         | 1 -
 tests/testthat/test_mvmr_local.R   | 1 -
 tests/testthat/test_otherformats.R | 1 -
 tests/testthat/test_outcomes.R     | 1 -
 tests/testthat/test_rsq.r          | 9 ---------
 8 files changed, 16 deletions(-)

diff --git a/tests/testthat/test_add_metadata.r b/tests/testthat/test_add_metadata.r
index 4207df4f..7aa71c54 100644
--- a/tests/testthat/test_add_metadata.r
+++ b/tests/testthat/test_add_metadata.r
@@ -3,7 +3,6 @@ context("add metadata")
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()
-skip_on_ci()
 
 # get required data
 # d1 <- extract_instruments('ieu-a-2')
diff --git a/tests/testthat/test_instruments.R b/tests/testthat/test_instruments.R
index 4bde502e..0d2a5c06 100644
--- a/tests/testthat/test_instruments.R
+++ b/tests/testthat/test_instruments.R
@@ -3,7 +3,6 @@ context("Instruments")
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()
-skip_on_ci()
 
 test_that("server and mrinstruments 1", {
 	# no no
diff --git a/tests/testthat/test_ld.R b/tests/testthat/test_ld.R
index fb386c1d..c763218c 100644
--- a/tests/testthat/test_ld.R
+++ b/tests/testthat/test_ld.R
@@ -3,7 +3,6 @@ context("ld")
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()
-skip_on_ci()
 
 # extract some data
 a <- try(extract_instruments("ieu-a-2", clump=FALSE))
diff --git a/tests/testthat/test_mvmr.R b/tests/testthat/test_mvmr.R
index dbc6658c..b74ee7e1 100644
--- a/tests/testthat/test_mvmr.R
+++ b/tests/testthat/test_mvmr.R
@@ -1,6 +1,5 @@
 context("mvmr")
 
-skip_on_ci()
 skip_on_cran()
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
diff --git a/tests/testthat/test_mvmr_local.R b/tests/testthat/test_mvmr_local.R
index 4c2a636c..4446aadb 100644
--- a/tests/testthat/test_mvmr_local.R
+++ b/tests/testthat/test_mvmr_local.R
@@ -12,7 +12,6 @@ load(system.file("extdata", "test_add_mvmr_local.RData", package="TwoSampleMR"))
 test_that("mv exposure local", {
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
-	skip_on_ci()
 	skip_on_cran()
     f1 <- tempfile()
     f2 <- tempfile()
diff --git a/tests/testthat/test_otherformats.R b/tests/testthat/test_otherformats.R
index 28187514..6f5e0e12 100644
--- a/tests/testthat/test_otherformats.R
+++ b/tests/testthat/test_otherformats.R
@@ -13,7 +13,6 @@ test_that("MRInput", {
 
 test_that("MRInput with cor", {
   skip_on_cran()
-  skip_on_ci()
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
 	expect_warning(w <- dat_to_MRInput(dat, get_correlations=TRUE)[[1]])
diff --git a/tests/testthat/test_outcomes.R b/tests/testthat/test_outcomes.R
index da9d672c..5290503b 100644
--- a/tests/testthat/test_outcomes.R
+++ b/tests/testthat/test_outcomes.R
@@ -3,7 +3,6 @@ context("outcome")
 skip_if_offline()
 skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()
-skip_on_ci()
 
 a <- try(extract_instruments("ieu-a-7"))
 if(inherits(a, "try-error")) skip("Server issues")
diff --git a/tests/testthat/test_rsq.r b/tests/testthat/test_rsq.r
index 407cf201..b430a46a 100644
--- a/tests/testthat/test_rsq.r
+++ b/tests/testthat/test_rsq.r
@@ -13,7 +13,6 @@ test_that("exposure data 2", {
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
-  skip_on_ci()
   d <- try(extract_instruments(c('ieu-a-2', 'ieu-a-7')))
   if(inherits(d, "try-error")) skip("Server issues")
   d <- d %>% add_rsq()
@@ -27,7 +26,6 @@ test_that("outcome data 1", {
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
-  skip_on_ci()
   d <- try(extract_outcome_data(exposure$SNP, 'ieu-a-2'))
   if(inherits(d, "try-error")) skip("Server issues")
   d <- d %>% add_rsq()
@@ -39,7 +37,6 @@ test_that("outcome data 2", {
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
-  skip_on_ci()
   d <- try(extract_outcome_data(exposure$SNP, c('ieu-a-2', 'ieu-a-7')))
   if(inherits(d, "try-error")) skip("Server issues")
   d <- d %>% add_rsq()
@@ -51,7 +48,6 @@ test_that("dat 2", {
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
-  skip_on_ci()
   d <- try(make_dat(proxies=FALSE))
   if(inherits(d, "try-error")) skip("Server issues")
   d <- d %>% add_rsq()
@@ -63,8 +59,6 @@ test_that("dat ukb-d", {
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
-  skip_on_cran()
-  skip_on_ci()
   d <- try(make_dat(exposure="ukb-d-30710_irnt", proxies=FALSE))
   if(inherits(d, "try-error")) skip("Server issues")
   d <- d %>% add_rsq()
@@ -82,7 +76,6 @@ test_that("get_population_allele_frequency", {
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
-  skip_on_ci()
 	d <- try(extract_instruments("ieu-a-7"))
 	if(inherits(d, "try-error")) skip("Server issues")
 	d <- try(add_metadata(d))
@@ -98,7 +91,6 @@ test_that("get_population_allele_frequency", {
 
 test_that("bbj-a-1", {
   skip_on_cran()
-  skip_on_ci()
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   d <- try(extract_instruments('bbj-a-1'))
@@ -112,7 +104,6 @@ test_that("bsen vs pn", {
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
-  skip_on_ci()
   d <- try(extract_instruments("ieu-a-2"))
   if(inherits(d, "try-error")) skip("Server issues")
 	r1 <- get_r_from_bsen(d$beta.exposure, d$se.exposure, d$samplesize.exposure)

From 1d5c620b53567b3a31234a5274ef608ae0b72ffa Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 16:00:47 +0100
Subject: [PATCH 46/48] Add try() to catch server non-response

---
 tests/testthat/test_otherformats.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test_otherformats.R b/tests/testthat/test_otherformats.R
index 6f5e0e12..c469bd75 100644
--- a/tests/testthat/test_otherformats.R
+++ b/tests/testthat/test_otherformats.R
@@ -15,7 +15,8 @@ test_that("MRInput with cor", {
   skip_on_cran()
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
-	expect_warning(w <- dat_to_MRInput(dat, get_correlations=TRUE)[[1]])
+	w <- try(dat_to_MRInput(dat, get_correlations=TRUE)[[1]])
+	if (inherits(w, "try-error")) skip("Server issues")
 	expect_true(nrow(w@correlation) == length(w@betaX))
 })
 

From 433e7c46c451013e44e5c65073ea9985742ef730 Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 16:01:00 +0100
Subject: [PATCH 47/48] Add try() to catch server non-response

---
 tests/testthat/test_rsq.r | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test_rsq.r b/tests/testthat/test_rsq.r
index b430a46a..734649b7 100644
--- a/tests/testthat/test_rsq.r
+++ b/tests/testthat/test_rsq.r
@@ -28,7 +28,8 @@ test_that("outcome data 1", {
   skip_on_cran()
   d <- try(extract_outcome_data(exposure$SNP, 'ieu-a-2'))
   if(inherits(d, "try-error")) skip("Server issues")
-  d <- d %>% add_rsq()
+  d <- try(d %>% add_rsq())
+  if (inherits(d, "try-error")) skip("Server issues")
 	expect_true("rsq.outcome" %in% names(d))
 	expect_true("effective_n.outcome" %in% names(d))
 })
@@ -39,7 +40,8 @@ test_that("outcome data 2", {
   skip_on_cran()
   d <- try(extract_outcome_data(exposure$SNP, c('ieu-a-2', 'ieu-a-7')))
   if(inherits(d, "try-error")) skip("Server issues")
-  d <- d %>% add_rsq()
+  d <- try(d %>% add_rsq())
+  if(inherits(d, "try-error")) skip("Server issues")
 	expect_true("rsq.outcome" %in% names(d))
 	expect_true("effective_n.outcome" %in% names(d))
 })

From 74046aa8720ff7c9d4f7cdc340442a558a07c37e Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Sun, 30 Jun 2024 16:14:29 +0100
Subject: [PATCH 48/48] Skip 2 tests on CI

---
 tests/testthat/test_rsq.r | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/testthat/test_rsq.r b/tests/testthat/test_rsq.r
index 734649b7..89d62984 100644
--- a/tests/testthat/test_rsq.r
+++ b/tests/testthat/test_rsq.r
@@ -26,6 +26,7 @@ test_that("outcome data 1", {
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
+  skip_on_ci()
   d <- try(extract_outcome_data(exposure$SNP, 'ieu-a-2'))
   if(inherits(d, "try-error")) skip("Server issues")
   d <- try(d %>% add_rsq())
@@ -38,6 +39,7 @@ test_that("outcome data 2", {
   skip_if_offline()
   skip_if_offline(host = "api.opengwas.io")
   skip_on_cran()
+  skip_on_ci()
   d <- try(extract_outcome_data(exposure$SNP, c('ieu-a-2', 'ieu-a-7')))
   if(inherits(d, "try-error")) skip("Server issues")
   d <- try(d %>% add_rsq())