Merge pull request #307071 from Kupac/fix_immunotation

      buildInputs = [ cacert ] ++ attrs.buildInputs;

    });

    immunotation = let

      MHC41alleleList = fetchurl {

        url = "https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list";

        hash = "sha256-CRZ+0uHzcq5zK5eONucAChXIXO8tnq5sSEAS80Z7jhg=";

      };

      MHCII40alleleList = fetchurl {

        url = "https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list";

        hash = "sha256-K4Ic2NUs3P4IkvOODwZ0c4Yh8caex5Ih0uO5jXRHp40=";

      };

      # List of valid countries, regions and ethnic groups

      # The original page is changing a bit every day, but the relevant

      # content does not. Use archive.org to get a stable snapshot.

      # It can be updated from time to time, or when the package becomes

      # deficient. This may be difficult to know.

      # Update the snapshot date, and add id_ after it, as described here:

      # https://web.archive.org/web/20130806040521/http://faq.web.archive.org/page-without-wayback-code/

      validGeographics = fetchurl {

        url = "https://web.archive.org/web/20240418194005id_/http://www.allelefrequencies.net/hla6006a.asp";

        hash = "sha256-m7Wkmh/cPxeqn94LwoznIh+fcFXskmSGErUYj6kTqak=";

      };

    in old.immunotation.overrideAttrs (attrs: {

      patches = [ ./patches/immunotation.patch ];

      postPatch = ''

        substituteInPlace "R/external_resources_input.R" --replace-fail \

          "nix-NetMHCpan-4.1-allele-list" ${MHC41alleleList}

        substituteInPlace "R/external_resources_input.R" --replace-fail \

          "nix-NETMHCIIpan-4.0-alleles-name-list" ${MHCII40alleleList}

        substituteInPlace "R/AFND_interface.R" --replace-fail \

          "nix-valid-geographics" ${validGeographics}

      '';

    });

    rstan = old.rstan.overrideAttrs (attrs: {

      env = (attrs.env or { }) // {

        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";

diff --git a/R/AFND_interface.R b/R/AFND_interface.R

index b62e8e0..0f22d85 100644

--- a/R/AFND_interface.R

+++ b/R/AFND_interface.R

@@ -244,9 +244,9 @@ check_population <- function(hla_population) {

 #' @return list of valid countries, regions and ethnic origin

 #' @keywords internal

 get_valid_geographics <- function() {

-    url <- "http://www.allelefrequencies.net/hla6006a.asp?"

-    html_input <- getURL(url, read_method = "html")

-    

+    # http://www.allelefrequencies.net/hla6006a.asp?

+    html_input <- xml2::read_html("nix-valid-geographics")

+      

     rvest_tables <- rvest::html_table(html_input, fill = TRUE)

     # country

diff --git a/R/external_resources_input.R b/R/external_resources_input.R

index c4b1dc1..8fc5881 100644

--- a/R/external_resources_input.R

+++ b/R/external_resources_input.R

@@ -74,16 +74,17 @@ getURL <- function(URL, N.TRIES=2L,

 # MHC I

 # netmhcI_input_template is an internal variable containing list of valid 

 # NetMHCpan input alleles

-netmhcI_input_template <- getURL(

-    URL="https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list",

-    read_method = "delim", delim = "\t",

-    col_names = c("netmhc_input", "hla_chain_name", "HLA_gene"))

+netmhcI_input_template <- readr::read_delim(

+        # https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list

+	"nix-NetMHCpan-4.1-allele-list",

+	delim = "\t",

+	skip = 0,

+        col_names = c("netmhc_input", "hla_chain_name", "HLA_gene")

+    )

 # MHC II

-lines <- getURL(

-    URL = paste0("https://services.healthtech.dtu.dk/services/",

-    "NetMHCIIpan-4.0/alleles_name.list"),

-    read_method = "lines")

+# https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list

+lines <- readr::read_lines("nix-NETMHCIIpan-4.0-alleles-name-list")

 lines_rep <- stringr::str_replace_all(lines, "\t+|\\s\\s+", "\t")

 netmhcII_input_template <- suppressWarnings(

     suppressMessages(read.delim(textConnection(lines_rep), sep = "\t")))