fixed #23

MANIFEST.in

@@ -14,3 +14,4 @@ include bedboss/tokens/*
 include bedboss/tokens/*
 include bedboss/bbuploader/*
 include bedboss/refgenome_validator/chrom_sizes/*
+include bedboss/scripts/*

bedboss/bedboss.py

@@ -46,7 +46,10 @@ def requirements_check() -> None:
     """
     _LOGGER.info("Checking requirements...")
     subprocess.run(
-        ["bash", f"{os.path.dirname(os.path.abspath(__file__))}/requirements_test.sh"]
+        [
+            "bash",
+            f"{os.path.dirname(os.path.abspath(__file__))}/scripts/requirements_test.sh",
+        ]
     )
 
 

bedboss/cli.py

@@ -657,7 +657,9 @@ def install_requirements():
     import subprocess
 
     r_path = os.path.abspath(
-        os.path.join(os.path.dirname(os.path.realpath(__file__)), "installRdeps.R")
+        os.path.join(
+            os.path.dirname(os.path.realpath(__file__)), "scripts", "installRdeps.R"
+        )
     )
 
     subprocess.run(

bedboss/scripts/check_R_req.R

@@ -0,0 +1,43 @@
+check_required_packages <- function() {
+  # ANSI escape codes for colors
+  red <- "\033[31m"
+  green <- "\033[32m"
+  reset <- "\033[0m"
+
+  # List of required R packages
+  required_packages <- c(
+    "optparse", "devtools", "ensembldb", "ExperimentHub", "AnnotationHub",
+    "AnnotationFilter", "BSgenome", "GenomicFeatures", "GenomicDistributions",
+    "GenomicDistributionsData", "GenomeInfoDb", "tools", "R.utils", "LOLA", "conflicted"
+  )
+
+  # Check if each package is installed
+  missing_packages <- required_packages[!sapply(required_packages, requireNamespace, quietly = TRUE)]
+
+  # Get the installed packages
+  installed_packages <- required_packages[sapply(required_packages, requireNamespace, quietly = TRUE)]
+
+  # If there are missing packages, print them
+  if (length(missing_packages) > 0) {
+    cat(paste0(red, "The following packages are missing:\n", reset))
+    cat(paste0(red, missing_packages, collapse = "\n"), "\n", reset)  # Print missing packages vertically
+  } else {
+    cat(paste0(green, "All R required packages are installed.\n", reset))
+  }
+
+  # Print installed packages vertically
+  cat(paste0(green, "\nThe following packages are installed:\n", reset))
+  cat(paste0(green, installed_packages, collapse = "\n"), "\n", reset)  # Print installed packages vertically
+
+  # Return missing packages
+  return(missing_packages)
+}
+
+# Call the function
+missing_packages <- check_required_packages()
+
+# Optionally handle missing packages
+if (length(missing_packages) > 0) {
+  quit(status = 1)
+}
+quit(status = 0)

bedboss/requirements_test.sh → bedboss/scripts/requirements_test.sh

@@ -116,17 +116,36 @@ if ! is_executable "wigToBigWig"; then
     INSTALL_WARNINGS=$((INSTALL_WARNINGS+1))
 fi
 
-
-if is_executable "R"; then
+# Old requirements check
+#if is_executable "R"; then
+#
+#    echo -e "-----------------------------------------------------------"
+#    echo -e "Checking required R packages for bedstat...                            "
+#    echo -e "-----------------------------------------------------------"
+#    declare -a requiredRPackages=("optparse ""devtools" "ensembldb" "ExperimentHub" "AnnotationHub" "AnnotationFilter" "BSgenome" "GenomicFeatures" "GenomicDistributions" "GenomicDistributionsData" "GenomeInfoDb" "ensembldb" "tools" "R.utils" "LOLA" "conflicted")
+#    for package in "${requiredRPackages[@]}"; do
+#      if ! r_check_req $package; then
+#        INSTALL_ERROR=$((INSTALL_ERROR+1))
+#      fi
+#done
+#fi
+
+if is_executable "Rscript"; then
     echo -e "-----------------------------------------------------------"
     echo -e "Checking required R packages for bedstat...                            "
     echo -e "-----------------------------------------------------------"
-    declare -a requiredRPackages=("optparse ""devtools" "ensembldb" "ExperimentHub" "AnnotationHub" "AnnotationFilter" "BSgenome" "GenomicFeatures" "GenomicDistributions" "GenomicDistributionsData" "GenomeInfoDb" "ensembldb" "tools" "R.utils" "LOLA" "conflicted")
-    for package in "${requiredRPackages[@]}"; do
-      if ! r_check_req $package; then
-        INSTALL_ERROR=$((INSTALL_ERROR+1))
-      fi
-done
+
+    SCRIPT_DIR=$(dirname "$(realpath "$0")")
+#    echo "The script is located at: $SCRIPT_DIR"
+    Rscript "$SCRIPT_DIR/check_R_req.R"
+
+    if [ $? -eq 0 ]; then
+      echo "All required packages are installed."
+    else
+       echo $(fail "ERROR: Some R required packages are missing. Please install them.")
+      INSTALL_ERROR=$((INSTALL_ERROR+1))
+    fi
+
 fi
 
 echo "Number of WARNINGS: $INSTALL_WARNINGS"