Updates renv

UoMResearchIT · Mar 29, 2024 · 9e29081 · 9e29081
1 parent c001ec7
commit 9e29081
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Showing 3 changed files with 15 additions and 78 deletions.
diff --git a/db/R/data_preprocessing.R b/db/R/data_preprocessing.R
@@ -1,7 +1,11 @@
 #### Load libraries ####
 library(tidyr)
-library(readxl)
+library(openxlsx)
 library(SummarizedExperiment)
+library(QFeatures)
+library(dplyr)
+library(MsCoreUtils)
+
 
 
 #### Full pre-processing pipeline ####
@@ -54,7 +58,7 @@ preprocess_data <- function(raw_data_path = "", dataset_name = "", dataset_path
   # Load protein data
   print("Loading protein data...")
   protein_data <- tryCatch({
-    read_excel(dataset_path)
+    read.xlsx(dataset_path)
   }, error = function(e) {
     message("Error reading the Excel file:", conditionMessage(e))
   })

diff --git a/db/R/mqtt_client.R b/db/R/mqtt_client.R
@@ -5,6 +5,7 @@
 # Load necessary libraries
 library(jsonlite)
 library(processx)
+library(crayon)
 
 source("R/on_message.R")
 

diff --git a/db/renv.lock b/db/renv.lock
@@ -485,15 +485,15 @@
     },
     "boot": {
       "Package": "boot",
-      "Version": "1.3-28",
+      "Version": "1.3-30",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "graphics",
         "stats"
       ],
-      "Hash": "0baa960e3b49c6176a4f42addcbacc59"
+      "Hash": "96abeed416a286d4a0f52e550b612343"
     },
     "brio": {
       "Package": "brio",
@@ -518,18 +518,6 @@
       ],
       "Hash": "9f0e4fae4963ba775a5e5c520838c87b"
     },
-    "cellranger": {
-      "Package": "cellranger",
-      "Version": "1.1.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "rematch",
-        "tibble"
-      ],
-      "Hash": "f61dbaec772ccd2e17705c1e872e9e7c"
-    },
     "cli": {
       "Package": "cli",
       "Version": "3.6.2",
@@ -754,10 +742,10 @@
     },
     "fastmap": {
       "Package": "fastmap",
-      "Version": "1.1.0",
+      "Version": "1.1.1",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "77bd60a6157420d4ffa93b27cf6a58b8"
+      "Repository": "RSPM",
+      "Hash": "f7736a18de97dea803bde0a2daaafb27"
     },
     "formatR": {
       "Package": "formatR",
@@ -872,20 +860,6 @@
       ],
       "Hash": "8eb36c8125038e648e5d111c0d7b2ed4"
     },
-    "hms": {
-      "Package": "hms",
-      "Version": "1.1.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "lifecycle",
-        "methods",
-        "pkgconfig",
-        "rlang",
-        "vctrs"
-      ],
-      "Hash": "b59377caa7ed00fa41808342002138f9"
-    },
     "htmltools": {
       "Package": "htmltools",
       "Version": "0.5.7",
@@ -1348,13 +1322,6 @@
       "Repository": "RSPM",
       "Hash": "a555924add98c99d2f411e37e7d25e9f"
     },
-    "prettyunits": {
-      "Package": "prettyunits",
-      "Version": "1.1.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Hash": "95ef9167b75dde9d2ccc3c7528393e7e"
-    },
     "processx": {
       "Package": "processx",
       "Version": "3.8.3",
@@ -1368,19 +1335,6 @@
       ],
       "Hash": "82d48b1aec56084d9438dbf98087a7e9"
     },
-    "progress": {
-      "Package": "progress",
-      "Version": "1.2.2",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R6",
-        "crayon",
-        "hms",
-        "prettyunits"
-      ],
-      "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061"
-    },
     "promises": {
       "Package": "promises",
       "Version": "1.2.1",
@@ -1423,28 +1377,6 @@
       ],
       "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc"
     },
-    "readxl": {
-      "Package": "readxl",
-      "Version": "1.4.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cellranger",
-        "cpp11",
-        "progress",
-        "tibble",
-        "utils"
-      ],
-      "Hash": "8cf9c239b96df1bbb133b74aef77ad0a"
-    },
-    "rematch": {
-      "Package": "rematch",
-      "Version": "2.0.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Hash": "cbff1b666c6fa6d21202f07e2318d4f1"
-    },
     "rematch2": {
       "Package": "rematch2",
       "Version": "2.1.2",
@@ -1660,9 +1592,9 @@
     },
     "tidyselect": {
       "Package": "tidyselect",
-      "Version": "1.2.0",
+      "Version": "1.2.1",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "cli",
@@ -1672,7 +1604,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "79540e5fcd9e0435af547d885f184fd5"
+      "Hash": "829f27b9c4919c16b593794a6344d6c0"
     },
     "tinytex": {
       "Package": "tinytex",