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rPackages.XLConnect: fix build (#458515)

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This commit is contained in:
Justin Bedő
2025-11-07 10:07:03 +11:00
committed by GitHub
parent d0770a20ec 686354856b
commit 51e3050d04
1 changed files with 78 additions and 1 deletions
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pkgs/development/r-modules/default.nix
+78 -1
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@@ -388,6 +388,7 @@ let
svaRetro = [ jbedo ];
StructuralVariantAnnotation = [ jbedo ];
RQuantLib = [ kupac ];
XLConnect = [ b-rodrigues ];
};
packagesWithRDepends = {
@@ -951,7 +952,6 @@ let
zlib
libxml2.dev
];
XLConnect = [ pkgs.jdk ];
xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ pkgs.perl ];
XML = with pkgs; [
libtool
@@ -2557,6 +2557,83 @@ let
'';
});
XLConnect =
let
poi-ooxml-full = fetchurl {
url = "https://repo1.maven.org/maven2/org/apache/poi/poi-ooxml-full/5.4.1/poi-ooxml-full-5.4.1.jar";
hash = "sha256-xRsFFlXVjXTV64nn03NscFLCV09Dx52wyKg60hb23Tc=";
};
poi-ooxml = fetchurl {
url = "https://repo1.maven.org/maven2/org/apache/poi/poi-ooxml/5.4.1/poi-ooxml-5.4.1.jar";
hash = "sha256-/SAMnm901wQWCpfp1SBBmV7YdDlFRTAAHt2SBojxn1M=";
};
poi = fetchurl {
url = "https://repo1.maven.org/maven2/org/apache/poi/poi/5.4.1/poi-5.4.1.jar";
hash = "sha256-2lq/QtpGBMWnvKOJVq9unW8ZbZttTLfqvuT0gLWA1QU=";
};
commons-compress = fetchurl {
url = "https://repo1.maven.org/maven2/org/apache/commons/commons-compress/1.27.1/commons-compress-1.27.1.jar";
hash = "sha256-KT2A9UtTa3QJXc1+o88KKbv8NAJRkoEzJJX0Qg03DRY=";
};
commons-lang3 = fetchurl {
url = "https://repo1.maven.org/maven2/org/apache/commons/commons-lang3/3.16.0/commons-lang3-3.16.0.jar";
hash = "sha256-CHCd101gK3Bc5AF9JlRCEAVqS6WD1bIMCTc0Bv56APg=";
};
xmlbeans = fetchurl {
url = "https://repo1.maven.org/maven2/org/apache/xmlbeans/xmlbeans/5.3.0/xmlbeans-5.3.0.jar";
hash = "sha256-bMado7TTW4PF5HfNTauiBORBCYM+NK8rmoosh4gomRc=";
};
commons-collections4 = fetchurl {
url = "https://repo1.maven.org/maven2/org/apache/commons/commons-collections4/4.4/commons-collections4-4.4.jar";
hash = "sha256-Hfi5QwtcjtFD14FeQD4z71NxskAKrb6b2giDdi4IRtE=";
};
commons-math3 = fetchurl {
url = "https://repo1.maven.org/maven2/org/apache/commons/commons-math3/3.6.1/commons-math3-3.6.1.jar";
hash = "sha256-HlbXsFjSi2Wr0la4RY44hbZ0wdWI+kPNfRy7nH7yswg=";
};
log4j-api = fetchurl {
url = "https://repo1.maven.org/maven2/org/apache/logging/log4j/log4j-api/2.24.3/log4j-api-2.24.3.jar";
hash = "sha256-W0oKDNDnUd7UMcFiRCvb3VMyjR+Lsrrl/Bu+7g9m2A8=";
};
commons-codec = fetchurl {
url = "https://repo1.maven.org/maven2/commons-codec/commons-codec/1.18.0/commons-codec-1.18.0.jar";
hash = "sha256-ugBfMEzvkqPe3iSjitWsm4r8zw2PdYOdbBM4Y0z39uQ=";
};
commons-io = fetchurl {
url = "https://repo1.maven.org/maven2/commons-io/commons-io/2.18.0/commons-io-2.18.0.jar";
hash = "sha256-88oPjWPEDiOlbVQQHGDV7e4Ta0LYS/uFvHljCTEJz4s=";
};
SparseBitSet = fetchurl {
url = "https://repo1.maven.org/maven2/com/zaxxer/SparseBitSet/1.3/SparseBitSet-1.3.jar";
hash = "sha256-92uFrbDAByGuJnt8/eTaf3HTEhzCFgyfwAwMifjFPIo=";
};
in
old.XLConnect.overrideAttrs (attrs: {
preConfigure = ''
cp ${poi-ooxml-full} inst/java/poi-ooxml-full-5.4.1.jar
cp ${poi-ooxml} inst/java/poi-ooxml-5.4.1.jar
cp ${poi} inst/java/poi-5.4.1.jar
cp ${commons-compress} inst/java/commons-compress-1.27.1.jar
cp ${commons-lang3} inst/java/commons-lang3-3.16.0.jar
cp ${xmlbeans} inst/java/xmlbeans-5.3.0.jar
cp ${commons-collections4} inst/java/commons-collections4-4.4.jar
cp ${commons-math3} inst/java/commons-math3-3.6.1.jar
cp ${log4j-api} inst/java/log4j-api-2.24.3.jar
cp ${commons-codec} inst/java/commons-codec-1.18.0.jar
cp ${commons-io} inst/java/commons-io-2.18.0.jar
cp ${SparseBitSet} inst/java/SparseBitSet-1.3.jar
'';
postPatch = ''
substituteInPlace R/onLoad.R \
--replace-fail 'system2("java",' 'system2("${lib.getExe pkgs.jre_headless}",'
# Misleading startup message, JARs are downloaded at build-time
substituteInPlace R/onAttach.R \
--replace-fail 'if(file.exists(file.path(libname, pkgname, ".fail"))){' 'if(FALSE){'
'';
});
immunotation =
let
MHC41alleleList = fetchurl {