From 07fe20ffbb95f13d216c9e0ebce9ad18db5021d5 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 09:16:36 +1000
Subject: [PATCH 01/18] fix: checck_entry function not handling missing Y value
 correctly, threw error during examples when running cran checks

---
 R/check_entry.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/check_entry.R b/R/check_entry.R
index 417ab1ae..b5f9189c 100644
--- a/R/check_entry.R
+++ b/R/check_entry.R
@@ -202,8 +202,8 @@ Check.entry.pls = function(X, Y, ncomp, keepX, keepY, test.keepX, test.keepY,
     if (!(logratio %in% c("none", "CLR")))
         stop("Choose one of the two following logratio transformation: none or CLR")
     
-    # if DA and the unmapped Y has rows without associated class
-    if (DA) {
+    # if DA and the unmapped Y has rows without associated class, only run this check if Y is not null (ie multilevel)
+    if (DA && !is.null(Y)) {
       if (length(which(rowSums(Y)==0)) != 0) {
         stop("Unmapped Y contains samples with no associated class. May be caused by NAs in input Y vector")
       }

From 2fa2c1edfbce9989224209cf0b24ec2c7c734665 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 09:33:49 +1000
Subject: [PATCH 02/18] fix github action: only push to dockerhub on linux
 runner

---
 .github/workflows/actions.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 5ce30af0..72f62b8f 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -208,7 +208,7 @@ jobs:
         shell: bash
 
       - name: Push to DockerHub 📦
-        if: needs.versions.outputs.dockerise == 'true' && !contains(github.event.head_commit.message, 'skip-docker')
+        if: runner.os == 'Linux' && needs.versions.outputs.dockerise == 'true' && !contains(github.event.head_commit.message, 'skip-docker')
         uses: docker/build-push-action@v1
         with:
           username: ${{ secrets.DOCKER_USERNAME }}

From d8b5a0f8360d7c4750586c6749f7bd2f44972b34 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 09:41:04 +1000
Subject: [PATCH 03/18] github action: force schedule run to check CRAN
 rcmdchecks

---
 .github/workflows/actions.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 72f62b8f..81192d63 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -6,7 +6,8 @@ on:
     branches:
       - master
   schedule:
-    - cron: '0 8 * * 4'
+    - cron: '44 23 * * *'
+    #- cron: '0 8 * * 4'
 
 name: R-CMD-check
 

From 56a703a664a3dff0b14d13d4c0b9aa03dcd74fee Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 10:45:15 +1000
Subject: [PATCH 04/18] fix error in network examples during rcmdcheck cran:
 interactive plot should only be made in interactive session

---
 examples/network-examples.R | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/examples/network-examples.R b/examples/network-examples.R
index ff8dfb38..815c2448 100644
--- a/examples/network-examples.R
+++ b/examples/network-examples.R
@@ -26,10 +26,12 @@ show.edge.labels = FALSE)
 dev.off()
 
 
-## interactive 'cutoff'
-
-network(nutri.res, comp = 1:3, cutoff = 0.55, interactive = TRUE)
-## select the 'cutoff' and "see" the new network
+## interactive 'cutoff' - select the 'cutoff' and "see" the new network
+## only run this during an interactive session
+if (interactive()) {
+    network(nutri.res, comp = 1:3, cutoff = 0.55, interactive = TRUE)
+}
+dev.off()
 
 ## network representation for objects of class 'spls'
 data(liver.toxicity)

From 51a7002db64b7ad5451bdbe88e8bc5b3b253a4dc Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 10:46:48 +1000
Subject: [PATCH 05/18] force schedule actions in 3 mins

---
 .github/workflows/actions.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 81192d63..75dae63b 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -6,7 +6,7 @@ on:
     branches:
       - master
   schedule:
-    - cron: '44 23 * * *'
+    - cron: '49 0 * * *'
     #- cron: '0 8 * * 4'
 
 name: R-CMD-check

From f624703a7713285c93cecca6d1cd8f5ddcc55ea9 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 11:03:35 +1000
Subject: [PATCH 06/18] edit github actions so can trigger a scheduled action
 automatically for checking purposes

---
 .github/workflows/actions.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 75dae63b..a66b5988 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -5,9 +5,9 @@ on:
   pull_request:
     branches:
       - master
+  workflow_dispatch:  # Allow manual triggers
   schedule:
-    - cron: '49 0 * * *'
-    #- cron: '0 8 * * 4'
+    - cron: '0 8 * * 4'
 
 name: R-CMD-check
 
@@ -181,7 +181,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Check --as-cran ✅ ✅ 
-        if: github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics'
+        if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
         env:
           _R_CHECK_CRAN_INCOMING_: false
         run: |
@@ -219,7 +219,7 @@ jobs:
           build_args: BIOC_VERSION=${{ needs.versions.outputs.bioc }} 
 
       - name: Test coverage 🔍
-        if: github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics'
+        if: (github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics') || (github.event_name == 'workflow_dispatch' && github.repository == 'mixOmicsTeam/mixOmics')
         # the commands between 'set +e' and 'set -e' are run without throwing any error
         run: |
           set +e

From 8496ee769ef1830cd6d9a86e4575a6d7b5b5bead Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 12:57:00 +1000
Subject: [PATCH 07/18] fix example error plotting type

---
 R/S3methods-plot.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/S3methods-plot.R b/R/S3methods-plot.R
index d01704f5..56c0df3f 100644
--- a/R/S3methods-plot.R
+++ b/R/S3methods-plot.R
@@ -54,10 +54,10 @@ plot.pca  <- function(x,
 #' nutri.res <- rcc(X, Y, lambda1 = 0.064, lambda2 = 0.008)
 #' 
 #' ## 'pointplot' type scree
-#' plot(nutri.res) #(default)
+#' plot(nutri.res, type = "point") #(default)
 #' 
 #' \dontrun{
-#' plot(nutri.res, pch = 19, cex = 1.2,
+#' plot(nutri.res, type = "point", pch = 19, cex = 1.2,
 #' col = c(rep("red", 3), rep("darkblue", 18)))
 #' 
 #' ## 'barplot' type scree

From 96e2f216749a7c1c1f9544ff392933bf6da76f87 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 13:39:02 +1000
Subject: [PATCH 08/18] updated docs

---
 man/network.Rd  | 10 ++++++----
 man/plot.rcc.Rd |  4 ++--
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/man/network.Rd b/man/network.Rd
index 61eb04ab..4e53afa1 100644
--- a/man/network.Rd
+++ b/man/network.Rd
@@ -252,10 +252,12 @@ show.edge.labels = FALSE)
 dev.off()
 
 
-## interactive 'cutoff'
-
-network(nutri.res, comp = 1:3, cutoff = 0.55, interactive = TRUE)
-## select the 'cutoff' and "see" the new network
+## interactive 'cutoff' - select the 'cutoff' and "see" the new network
+## only run this during an interactive session
+if (interactive()) {
+    network(nutri.res, comp = 1:3, cutoff = 0.55, interactive = TRUE)
+}
+dev.off()
 
 ## network representation for objects of class 'spls'
 data(liver.toxicity)
diff --git a/man/plot.rcc.Rd b/man/plot.rcc.Rd
index a73f7ccb..71e57d02 100644
--- a/man/plot.rcc.Rd
+++ b/man/plot.rcc.Rd
@@ -26,10 +26,10 @@ Y <- nutrimouse$gene
 nutri.res <- rcc(X, Y, lambda1 = 0.064, lambda2 = 0.008)
 
 ## 'pointplot' type scree
-plot(nutri.res) #(default)
+plot(nutri.res, type = "point") #(default)
 
 \dontrun{
-plot(nutri.res, pch = 19, cex = 1.2,
+plot(nutri.res, type = "point", pch = 19, cex = 1.2,
 col = c(rep("red", 3), rep("darkblue", 18)))
 
 ## 'barplot' type scree

From e89f2799cd28f75bfe4d872ce444a3842a8c2293 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 13:39:21 +1000
Subject: [PATCH 09/18] rgl required package due for 3D plots

---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c0c9882d..b66a96c2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -25,13 +25,13 @@ Imports:
     ggrepel,
     BiocParallel,
     utils,
-    gsignal
+    gsignal,
+    rgl
 Suggests: 
     BiocStyle,
     knitr,
     rmarkdown,
     testthat,
-    rgl,
     microbenchmark,
     magick
 Authors@R: 

From 5571abf26ba791eabd8fa19e457b0430f4301391 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 13:39:58 +1000
Subject: [PATCH 10/18] fixed util function used inside tune.block.splda which
 threw incorrect indY error

---
 R/utils.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 02e75921..3859fb39 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -472,9 +472,9 @@ nearZeroVar = function (x, freqCut = 95/5, uniqueCut = 10)
     if (!all(is.list(X) && length(unique(names(X))) == length(X)))
         stop("'X' must be a named list. See documentation.", call. = FALSE)
     
-    if ((missing(indY) || is.null(indY)) ) {
+    if ( missing(indY) || is.null(indY) || isTRUE(tryCatch(is.integer(as.integer(indY)) && indY > length(X))) ){
         indY <- length(X) + 1
-        X <- c(X, list(Y = matrix())) ## just so we have Y in X for design
+        X <- c(X, list(Y = matrix())) ## just so we have Y in X for design, indY may be > X as has already been used to extract Y in wrapper function e.g. in tune.block.splda
     }
     
     blocks <- names(X)

From a9cdf10c1e358bffc4616934ade2421a8a1718b9 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 13:41:01 +1000
Subject: [PATCH 11/18] removed typo

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

diff --git a/R/utils.R b/R/utils.R
index 3859fb39..028cbd62 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -474,7 +474,7 @@ nearZeroVar = function (x, freqCut = 95/5, uniqueCut = 10)
     
     if ( missing(indY) || is.null(indY) || isTRUE(tryCatch(is.integer(as.integer(indY)) && indY > length(X))) ){
         indY <- length(X) + 1
-        X <- c(X, list(Y = matrix())) ## just so we have Y in X for design, indY may be > X as has already been used to extract Y in wrapper function e.g. in tune.block.splda
+        X <- c(X, list(Y = matrix())) ## just so we have Y in X for design, ind
     }
     
     blocks <- names(X)

From 6bb2173f845b3143178500424d37f0761bde88e9 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 14:38:52 +1000
Subject: [PATCH 12/18] fixed error with plotloading when plot set to FALSE

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

diff --git a/R/plotLoadings.R b/R/plotLoadings.R
index 137a9d70..ee85a46b 100644
--- a/R/plotLoadings.R
+++ b/R/plotLoadings.R
@@ -466,9 +466,8 @@ plotLoadings.mixo_plsda <-
                                title = paste(legend.title),
                                cex = size.legend)
                     }
-                    
-                    contrib.df <- c(contrib.df, list(df))
                 } # end if plot
+                contrib.df <- c(contrib.df, list(df))
             }
             
             names(contrib.df) <- block

From fd81e9f53982b9cc107bf6fe25a6fc21802cec03 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 14:46:27 +1000
Subject: [PATCH 13/18] error in plotloading example code, as outputted
 plotloadings is a list of df (one per block)

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

diff --git a/examples/plotLoadings-examples.R b/examples/plotLoadings-examples.R
index 79669a69..a785c5ea 100644
--- a/examples/plotLoadings-examples.R
+++ b/examples/plotLoadings-examples.R
@@ -58,7 +58,7 @@ name.var = name.var, size.name = 0.5,complete.name.var=TRUE, contrib = "max")
 # look at the contribution (median) for each variable
 plot.contrib = plotLoadings(splsda.liver, comp = 2, method = 'median', plot = FALSE,
 contrib = "max")
-head(plot.contrib[,1:4])
+head(plot.contrib[[1]][,1:4])
 # change the title of the legend and title name
 plotLoadings(splsda.liver, comp = 2, method = 'median', legend.title = 'Time',
 title = 'Contribution plot', contrib = "max")

From 20e1a4e0fc92dbf2f03d0472b2f30acbd3abb0b7 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 14:52:13 +1000
Subject: [PATCH 14/18] plot loadings example description

---
 man/plotLoadings.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/plotLoadings.Rd b/man/plotLoadings.Rd
index 729a6bcd..318d85c1 100644
--- a/man/plotLoadings.Rd
+++ b/man/plotLoadings.Rd
@@ -482,7 +482,7 @@ name.var = name.var, size.name = 0.5,complete.name.var=TRUE, contrib = "max")
 # look at the contribution (median) for each variable
 plot.contrib = plotLoadings(splsda.liver, comp = 2, method = 'median', plot = FALSE,
 contrib = "max")
-head(plot.contrib[,1:4])
+head(plot.contrib[[1]][,1:4])
 # change the title of the legend and title name
 plotLoadings(splsda.liver, comp = 2, method = 'median', legend.title = 'Time',
 title = 'Contribution plot', contrib = "max")

From d26fec5c7f63cbaaed38bfd15eb54e7c39321f9b Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 14:54:25 +1000
Subject: [PATCH 15/18] fix error data not loaded in splsda example

---
 examples/splsda-examples.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/examples/splsda-examples.R b/examples/splsda-examples.R
index 47744e9b..ac8ccca3 100644
--- a/examples/splsda-examples.R
+++ b/examples/splsda-examples.R
@@ -67,6 +67,7 @@ plotIndiv(splsda.liver, ind.names = Y, ellipse = TRUE, legend = TRUE)
 ## Fifth example: 16S data with multilevel decomposion and log ratio transformation
 # ------------------------------------------------
 
+data(diverse.16S)
 splsda.16S = splsda(
 X = diverse.16S$data.TSS,  # TSS normalised data
 Y =  diverse.16S$bodysite,

From 27c20377b27ba1c04bae947c9d8d1b4739efd670 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 15:10:55 +1000
Subject: [PATCH 16/18] doc loading data in splsda example

---
 man/splsda.Rd | 1 +
 1 file changed, 1 insertion(+)

diff --git a/man/splsda.Rd b/man/splsda.Rd
index c199bd6e..56752a62 100644
--- a/man/splsda.Rd
+++ b/man/splsda.Rd
@@ -170,6 +170,7 @@ plotIndiv(splsda.liver, ind.names = Y, ellipse = TRUE, legend = TRUE)
 ## Fifth example: 16S data with multilevel decomposion and log ratio transformation
 # ------------------------------------------------
 
+data(diverse.16S)
 splsda.16S = splsda(
 X = diverse.16S$data.TSS,  # TSS normalised data
 Y =  diverse.16S$bodysite,

From c508c19726159dfb9012217a6b3ee1bd10f79350 Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 15:11:26 +1000
Subject: [PATCH 17/18] for examples using parallelisation, set up so rcmdcheck
 limit on number of cores is respected

---
 examples/tune.block.splsda-examples.R | 7 +++++--
 examples/tune.spca-examples.R         | 7 ++++---
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/examples/tune.block.splsda-examples.R b/examples/tune.block.splsda-examples.R
index 96f0bc51..67ce833a 100644
--- a/examples/tune.block.splsda-examples.R
+++ b/examples/tune.block.splsda-examples.R
@@ -28,8 +28,11 @@ subset <- mixOmics:::stratified.subsampling(breast.TCGA$data.train$subtype, fold
 data <- lapply(data, function(omic) omic[subset,])
 Y <- breast.TCGA$data.train$subtype[subset]
 ## ---- run
-## setup cluster - use SnowParam() on Widnows
-BPPARAM <- BiocParallel::MulticoreParam(workers = parallel::detectCores()-1)
+# Check if the environment variable exists (during R CMD check) and limit cores accordingly
+max_cores <- if (Sys.getenv("_R_CHECK_LIMIT_CORES_") != "") 2 else parallel::detectCores() - 1
+# Setup the parallel backend with the appropriate number of workers
+BPPARAM <- BiocParallel::MulticoreParam(workers = max_cores)
+
 tune <- tune.block.splsda(
     X = data,
     Y = Y,
diff --git a/examples/tune.spca-examples.R b/examples/tune.spca-examples.R
index 2e35ad19..9ca88fd2 100644
--- a/examples/tune.spca-examples.R
+++ b/examples/tune.spca-examples.R
@@ -12,9 +12,10 @@ tune.spca.res
 plot(tune.spca.res)
 \dontrun{
 ## parallel processing using BiocParallel on repeats with more workers (cpus)
-## You can use BiocParallel::MulticoreParam() on non_Windows machines 
-## for faster computation
-BPPARAM <- BiocParallel::SnowParam(workers = max(parallel::detectCores()-1, 2))
+# Check if the environment variable exists (during R CMD check) and limit cores accordingly
+max_cores <- if (Sys.getenv("_R_CHECK_LIMIT_CORES_") != "") 2 else parallel::detectCores() - 1
+# Setup the parallel backend with the appropriate number of workers
+BPPARAM <- BiocParallel::MulticoreParam(workers = max_cores)
 tune.spca.res <- tune.spca(
     X = nutrimouse$lipid,
     ncomp = 2,

From df14c296dfd0e5984700d7441531882ba8f5999b Mon Sep 17 00:00:00 2001
From: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: Fri, 4 Oct 2024 15:27:28 +1000
Subject: [PATCH 18/18] documentation for updated examples

---
 man/tune.block.splsda.Rd | 7 +++++--
 man/tune.spca.Rd         | 7 ++++---
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/man/tune.block.splsda.Rd b/man/tune.block.splsda.Rd
index 03818481..7381b228 100644
--- a/man/tune.block.splsda.Rd
+++ b/man/tune.block.splsda.Rd
@@ -206,8 +206,11 @@ subset <- mixOmics:::stratified.subsampling(breast.TCGA$data.train$subtype, fold
 data <- lapply(data, function(omic) omic[subset,])
 Y <- breast.TCGA$data.train$subtype[subset]
 ## ---- run
-## setup cluster - use SnowParam() on Widnows
-BPPARAM <- BiocParallel::MulticoreParam(workers = parallel::detectCores()-1)
+# Check if the environment variable exists (during R CMD check) and limit cores accordingly
+max_cores <- if (Sys.getenv("_R_CHECK_LIMIT_CORES_") != "") 2 else parallel::detectCores() - 1
+# Setup the parallel backend with the appropriate number of workers
+BPPARAM <- BiocParallel::MulticoreParam(workers = max_cores)
+
 tune <- tune.block.splsda(
     X = data,
     Y = Y,
diff --git a/man/tune.spca.Rd b/man/tune.spca.Rd
index 9856cf2b..9ec18317 100644
--- a/man/tune.spca.Rd
+++ b/man/tune.spca.Rd
@@ -88,9 +88,10 @@ tune.spca.res
 plot(tune.spca.res)
 \dontrun{
 ## parallel processing using BiocParallel on repeats with more workers (cpus)
-## You can use BiocParallel::MulticoreParam() on non_Windows machines 
-## for faster computation
-BPPARAM <- BiocParallel::SnowParam(workers = max(parallel::detectCores()-1, 2))
+# Check if the environment variable exists (during R CMD check) and limit cores accordingly
+max_cores <- if (Sys.getenv("_R_CHECK_LIMIT_CORES_") != "") 2 else parallel::detectCores() - 1
+# Setup the parallel backend with the appropriate number of workers
+BPPARAM <- BiocParallel::MulticoreParam(workers = max_cores)
 tune.spca.res <- tune.spca(
     X = nutrimouse$lipid,
     ncomp = 2,