rPackages: fix changed hashes (#527156)

pkgs/applications/science/math/R/default.nix

@@ -45,7 +45,7 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "R";
-  version = "4.5.3";
+  version = "4.6.0";
 
   src =
     let
@@ -53,7 +53,7 @@ stdenv.mkDerivation (finalAttrs: {
     in
     fetchurl {
       url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
-      hash = "sha256-qlwe1Ck8cnGsUT1lRnA1asDopq1eQr4BQ2XREVC1uPI=";
+      hash = "sha256-uNybRUNmDHtZa4eTjfUyOUNQNgl2Un00QijuDtEuRew=";
     };
 
   outputs = [

pkgs/development/r-modules/bioc-annotation-packages.json

@@ -1,6 +1,6 @@
 {
   "extraArgs": {
-    "biocVersion": "3.22"
+    "biocVersion": "3.23"
   },
   "packages": {
     "AHCytoBands": {
@@ -737,8 +737,8 @@
     },
     "BioMartGOGeneSets": {
       "name": "BioMartGOGeneSets",
-      "version": "0.99.11",
-      "sha256": "1ack8v1q0zg15gs816n9f4pwrzrpsv4va6j0r8847pw0pvavwpiq",
+      "version": "0.99.12",
+      "sha256": "11x00v18vd5ppm9asg120dmhmqamzsacy64v3kmmxfn7rhxl25b2",
       "depends": ["GenomicRanges", "S4Vectors"]
     },
     "CENTREannotation": {
@@ -749,8 +749,8 @@
     },
     "CTCF": {
       "name": "CTCF",
-      "version": "0.99.13",
-      "sha256": "097w2rad5fxyg2dkghz6ws93q1l7hlc6f9dnw1n30gs2bdv5hbyb",
+      "version": "0.99.14",
+      "sha256": "06nyz5758mq04hzvc7bl0ld2d173zabs9xyhva01y92b19yy8nfp",
       "depends": []
     },
     "ChemmineDrugs": {
@@ -887,14 +887,14 @@
     },
     "GO_db": {
       "name": "GO.db",
-      "version": "3.22.0",
-      "sha256": "1liyl1ic2d08an0h6yxllggkv9n8vyp1bfjwvqzk5ana17lzmimf",
+      "version": "3.23.1",
+      "sha256": "0ays2n3jivigpr7m3y3rba8gjyqr7g3qxdslppww0z0zzm4m808z",
       "depends": ["AnnotationDbi"]
     },
     "GeneSummary": {
       "name": "GeneSummary",
-      "version": "0.99.6",
-      "sha256": "0h6afrjb00afrcw6mwslxp7cmwfzp4qfxh0aa4f41kfjd3cymmp5",
+      "version": "0.99.7",
+      "sha256": "0pl843r230cgq0nh5pwp19zz823dwdv789kfcgdhylijx3h2ymfk",
       "depends": []
     },
     "GenomeInfoDbData": {
@@ -1241,8 +1241,8 @@
     },
     "Orthology_eg_db": {
       "name": "Orthology.eg.db",
-      "version": "3.22.0",
-      "sha256": "14wng7izmr7wx3yimjlvmk87vf1z3z0n88y2nghn8a2iqci1rl3s",
+      "version": "3.23.0",
+      "sha256": "0640jwylw67cw8sylmyfcqm8cak5i2bx9k925bwm0bjmayxl8yw3",
       "depends": ["AnnotationDbi"]
     },
     "PANTHER_db": {
@@ -1673,8 +1673,8 @@
     },
     "UniProtKeywords": {
       "name": "UniProtKeywords",
-      "version": "0.99.7",
-      "sha256": "10id2lk2mbccay7p44pk58zhkiqc58x237qr76plivgpcc8xhjzq",
+      "version": "0.99.8",
+      "sha256": "1mhbhar70acwgjmlfkfrqc2hskqvbgsaf9xlzv8ph66x6gvbyqb7",
       "depends": []
     },
     "XtraSNPlocs_Hsapiens_dbSNP144_GRCh37": {
@@ -2093,8 +2093,8 @@
     },
     "excluderanges": {
       "name": "excluderanges",
-      "version": "0.99.10",
-      "sha256": "0j9njpnbh731ffimr1sbvix3wsivnh9nwxg6sbrpwp8gl0pnl7r0",
+      "version": "0.99.11",
+      "sha256": "1czr9hr84hzwa7fyzm51425nphy0b9h5yfvgkij5v8qgq565w02a",
       "depends": ["GenomicRanges"]
     },
     "fitCons_UCSC_hg19": {
@@ -2513,8 +2513,8 @@
     },
     "hpAnnot": {
       "name": "hpAnnot",
-      "version": "1.1.1",
-      "sha256": "0bkfcj9igi7ylhf3arszqnqzaxsxvfv2gn2smzx6ymzq5a8sc0yg",
+      "version": "1.1.3",
+      "sha256": "0gnir407flzzkkljxf2brqrw2kaycl8azi0wc5yn1fhl7x5zidq1",
       "depends": ["AnnotationHub"]
     },
     "hs25kresogen_db": {
@@ -3749,20 +3749,20 @@
     },
     "org_Hs_eg_db": {
       "name": "org.Hs.eg.db",
-      "version": "3.22.0",
-      "sha256": "0bia1ppxnyjpw4p3rk19q1l8rrcraccpz4w69f3ja0q0im0xrgfi",
+      "version": "3.23.1",
+      "sha256": "1zlwsk1hq40xi8xd7wc974jp8gky6x7icc9788ch77glbik201j7",
       "depends": ["AnnotationDbi"]
     },
     "org_Mm_eg_db": {
       "name": "org.Mm.eg.db",
-      "version": "3.22.0",
-      "sha256": "16liabdbkfqzhna3rw1zgf777r3xm8knrbvy0181c2nsn2jkxsv3",
+      "version": "3.23.0",
+      "sha256": "0i252737v6wk0im41gnksz4qkzf286kwgfq60yqc1mfva77m8yjh",
       "depends": ["AnnotationDbi"]
     },
     "org_Mmu_eg_db": {
       "name": "org.Mmu.eg.db",
-      "version": "3.22.0",
-      "sha256": "0ga0c9635pkigmr0l9vazh3qdpyxki1y8l7mbgcp1y8sfkyjn33c",
+      "version": "3.23.0",
+      "sha256": "08l4bckvn42yjgpkcmq87c1c2z4g8cfjc9jm5ibb84v5ffjw92ij",
       "depends": ["AnnotationDbi"]
     },
     "org_Mxanthus_db": {
@@ -3779,14 +3779,14 @@
     },
     "org_Pt_eg_db": {
       "name": "org.Pt.eg.db",
-      "version": "3.22.0",
-      "sha256": "1i67vccx3a6zak34nwdhrbhm7hkjz9qbai9jvwrlql6z8xc6n6q0",
+      "version": "3.23.0",
+      "sha256": "1hfvrv2n9gc0h4s6ql4lv8q8qjf75c4y5p2hlplhphzi38j54vhl",
       "depends": ["AnnotationDbi"]
     },
     "org_Rn_eg_db": {
       "name": "org.Rn.eg.db",
-      "version": "3.22.0",
-      "sha256": "0vqpmbivxd1yvapa5gz9mrxlk6ivrzak55dw2sfjm8sl308rmaj4",
+      "version": "3.23.0",
+      "sha256": "1j1gs8bk1a247shhs5z41s4pk6hw4ssy7405fv5q16m5ilpwgc1g",
       "depends": ["AnnotationDbi"]
     },
     "org_Sc_sgd_db": {
@@ -3797,14 +3797,14 @@
     },
     "org_Ss_eg_db": {
       "name": "org.Ss.eg.db",
-      "version": "3.22.0",
-      "sha256": "03qlbkvxfmdgpl8dwx72msd9asx12izvq2vmidqfyipyr7r79cbm",
+      "version": "3.23.0",
+      "sha256": "0ijn7dfh485lww1d9bp8j40fcjr1lx8vdnlq6ydwq3ni4bifkzqp",
       "depends": ["AnnotationDbi"]
     },
     "org_Xl_eg_db": {
       "name": "org.Xl.eg.db",
-      "version": "3.22.0",
-      "sha256": "1h8jvdzhpp9d4zaaczhmg6hk32p77l63v3095ln58rhy9m18pg0f",
+      "version": "3.23.0",
+      "sha256": "1w856a5hkp9a5g41nd69xwvzaf1nmq7zqjsn7w5p1i2zsxv1i1k1",
       "depends": ["AnnotationDbi"]
     },
     "paeg1acdf": {
@@ -5111,8 +5111,8 @@
     },
     "reactome_db": {
       "name": "reactome.db",
-      "version": "1.95.0",
-      "sha256": "1b87byr45cmqa7jyd5fw3askmrzfhdljjp2d7jcmm88baf45mfg6",
+      "version": "1.96.0",
+      "sha256": "0b43ri3clg6ynp197vy24936n762k0f43v9m51g1lar2w4qc2zhb",
       "depends": ["AnnotationDbi"]
     },
     "rgu34a_db": {

pkgs/development/r-modules/default.nix

@@ -765,7 +765,9 @@ let
     ];
     RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
-    Rhdf5lib = with pkgs; [ zlib.dev ];
+    Rhdf5lib = with pkgs; [
+      cmake
+    ];
     Rhpc = with pkgs; [
       zlib
       bzip2.dev
@@ -821,7 +823,10 @@ let
     rpanel = [ pkgs.tclPackages.bwidget ];
     Rpoppler = [ pkgs.poppler ];
     RPostgreSQL = with pkgs; [ libpq.pg_config ];
-    RProtoBuf = [ pkgs.protobuf ];
+    RProtoBuf = with pkgs; [
+      protobuf
+      abseil-cpp.dev
+    ];
     rsamplr = with pkgs; [
       cargo
       rustc
@@ -865,6 +870,10 @@ let
       cargo
       rustc
     ];
+    tinyimg = with pkgs; [
+      cargo
+      rustc
+    ];
     caugi = with pkgs; [
       cargo
       rustc
@@ -966,6 +975,7 @@ let
       fontconfig.dev
       freetype.dev
     ];
+    rlas = [ pkgs.pkg-config ];
     TAQMNGR = [ pkgs.zlib.dev ];
     TDA = [ pkgs.gmp ];
     tesseract = with pkgs; [
@@ -1227,10 +1237,16 @@ let
       xz.dev
       zlib.dev
     ];
+    fs = [ pkgs.libuv ];
     pgenlibr = [ pkgs.zlib.dev ];
     fftw = [ pkgs.pkg-config ];
     gdtools = [ pkgs.pkg-config ];
     archive = [ pkgs.libarchive ];
+    lpsymphony = with pkgs; [
+      symphony
+      cgl
+      clp
+    ];
     gdalcubes = with pkgs; [
       proj.dev
       gdal
@@ -1251,6 +1267,10 @@ let
       fftw.dev
       pkg-config
     ];
+    Rhdf5lib = with pkgs; [
+      curl
+      zlib.dev
+    ];
     GRAB = [ pkgs.zlib.dev ];
     jqr = [ pkgs.jq.out ];
     kza = [ pkgs.pkg-config ];
@@ -1541,7 +1561,13 @@ let
     redux = [ pkgs.hiredis ];
     RmecabKo = [ pkgs.mecab ];
     markets = [ pkgs.gsl ];
-    rlas = [ pkgs.boost ];
+    rlas = with pkgs; [
+      boost
+      gdal
+      proj
+      sqlite
+      geos
+    ];
     bgx = [ pkgs.boost ];
     PoissonBinomial = [ pkgs.fftw.dev ];
     poisbinom = [ pkgs.fftw.dev ];
@@ -1947,6 +1973,10 @@ let
       postPatch = "patchShebangs configure";
     });
 
+    fixest = old.fixest.overrideAttrs (attrs: {
+      postPatch = "patchShebangs configure";
+    });
+
     arcgisplaces = old.arcgisplaces.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
@@ -1979,6 +2009,10 @@ let
       postPatch = "patchShebangs configure";
     });
 
+    ramr = old.ramr.overrideAttrs (attrs: {
+      postPatch = "patchShebangs configure";
+    });
+
     roxigraph = old.roxigraph.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         LIBCLANG_PATH = "${lib.getLib pkgs.libclang}/lib";
@@ -2440,6 +2474,10 @@ let
       '';
     });
 
+    RProtoBuf = old.RProtoBuf.overrideAttrs (attrs: {
+      configureFlags = [ "ac_cv_prog_cxx_cxx11=" ];
+    });
+
     JavaGD = old.JavaGD.overrideAttrs (attrs: {
       preConfigure = ''
         export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
@@ -2948,7 +2986,10 @@ let
     );
 
     lpsymphony = old.lpsymphony.overrideAttrs (attrs: {
-      preConfigure = ''
+      postPatch = ''
+        substituteInPlace configure \
+          --replace-fail '--libs SYMPHONY' '--libs symphony' \
+          --replace-fail '--cflags SYMPHONY' '--cflags symphony'
         patchShebangs configure
       '';
     });
@@ -3108,7 +3149,13 @@ let
 
     Rhdf5lib =
       let
-        hdf5 = pkgs.hdf5_1_10;
+        hdf5 = pkgs.hdf5.overrideAttrs (attrs: {
+          cmakeFlags = attrs.cmakeFlags ++ [ "-DHDF5_ENABLE_ROS3_VFD:BOOL=TRUE" ];
+          buildInputs = attrs.buildInputs ++ [ pkgs.curl.dev ];
+          postInstall = attrs.postInstall or "" + ''
+            cp src/libhdf5.settings $dev/lib
+          '';
+        });
       in
       old.Rhdf5lib.overrideAttrs (attrs: {
         propagatedBuildInputs = attrs.propagatedBuildInputs ++ [

pkgs/development/r-modules/patches/Rhdf5lib.patch

@@ -1,8 +1,8 @@
 diff --git a/R/zzz.R b/R/zzz.R
-index 97becd7..803ca39 100644
+index 2af2b3e..21ddc00 100644
 --- a/R/zzz.R
 +++ b/R/zzz.R
-@@ -20,7 +20,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+@@ -22,7 +22,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
  
    path <- Sys.getenv(
      x = "RHDF5LIB_RPATH",
@@ -10,70 +10,48 @@ index 97becd7..803ca39 100644
 +    unset = ""
    )
  
-   if (nzchar(.Platform$r_arch)) {
-@@ -59,7 +59,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
-                               sprintf('-L%s -lhdf5 %s',
+   sysname <- Sys.info()['sysname']
+@@ -47,7 +47,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5 %s', 
                                        patharch, winlibs)
                              }, {
 -                              sprintf('"%s/libhdf5.a"%s%s', 
-+                              sprintf('-lhdf5',
-                                       patharch, .getSzipLoc(patharch), .getDynamicLinks())
++                              sprintf('-lhdf5', 
+                                       patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
                              }
                       )
-@@ -70,7 +70,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
-                               sprintf('-L%s -lhdf5_cpp -lhdf5 %s',
+@@ -58,7 +58,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_cpp -lhdf5 %s', 
                                        patharch, winlibs)
                              }, {
 -                              sprintf('"%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
 +                              sprintf('-lhdf5_cpp -lhdf5',
-                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
                              }
                       )
-@@ -81,7 +81,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
-                               sprintf('-L%s -lhdf5_hl -lhdf5 %s',
+@@ -69,7 +69,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_hl -lhdf5 %s', 
                                        patharch, winlibs)
                              }, {
 -                              sprintf('"%s/libhdf5_hl.a" "%s/libhdf5.a"%s%s', 
-+                              sprintf('-lhdf5_hl -lhdf5',
-                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
++                              sprintf('-lhdf5_hl -lhdf5', 
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
                              }
                       )
-@@ -92,7 +92,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
-                               sprintf('-L%s -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 %s',
+@@ -80,7 +80,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 %s', 
                                        patharch, winlibs)
                              }, {
 -                              sprintf('"%s/libhdf5_hl_cpp.a" "%s/libhdf5_hl.a" "%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
 +                              sprintf('-lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5',
-                                       patharch, patharch, patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                                       patharch, patharch, patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks(patharch))
                              }
                       )
-@@ -124,6 +124,7 @@ getHdf5Version <- function() {
- #'
+@@ -113,6 +113,7 @@ getHdf5Version <- function() {
+ #' @noRd
  #' @keywords internal
- .getDynamicLinks <- function() {
+ .getDynamicLinks <- function(path) {
 +  return("")
-   sysname <- Sys.info()['sysname']
-   if(sysname == "Windows") {
-     links <- "-lz"
-diff --git a/src/Makevars.in b/src/Makevars.in
-index addb6a0..590784a 100644
---- a/src/Makevars.in
-+++ b/src/Makevars.in
-@@ -18,7 +18,7 @@ USER_LIB_DIR = ${R_PACKAGE_DIR}/lib${R_ARCH}/
- 
- PKG_CPPFLAGS = -I${USER_INCLUDE_DIR} ${ZLIB_INCLUDE}
- PKG_CFLAGS = ${ZLIB_LIB}
--PKG_LIBS = "${USER_LIB_DIR}libhdf5.a" @SZIP_LIB@ -lz
-+PKG_LIBS = -lhdf5 -lsz
- 
- 
- 
-@@ -26,7 +26,7 @@ all: $(SHLIB)
- 
- $(SHLIB): Rhdf5lib.o
- 
--Rhdf5lib.o: copy-hdf5 @COPY_SZIP@
-+Rhdf5lib.o:
- 
- copy-szip: copy-hdf5
- 	cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "${USER_LIB_DIR}"
+   settings_file <- file.path(path, "libhdf5.settings")
+   libhdf5_settings <- readLines(settings_file)
+   libstr <- grep("Extra libraries", x = libhdf5_settings, fixed = TRUE, value = TRUE) |> 

pkgs/development/r-modules/patches/rhdf5.patch

@@ -9,39 +9,3 @@ index 713b44c..704ac17 100644
  
  #PKG_CFLAGS = -Wall
  
-diff --git a/src/h5testLock.c b/src/h5testLock.c
-index b326444..5d58b4a 100644
---- a/src/h5testLock.c
-+++ b/src/h5testLock.c
-@@ -8,16 +8,16 @@ SEXP _h5fileLock(SEXP _file_name) {
-   int lk = -1;
- 
-   /* create the temporary file */
--  fd = HDopen(file_name, O_RDWR | O_CREAT | O_TRUNC, 0666);
-+  fd = open(file_name, O_RDWR | O_CREAT | O_TRUNC, 0666);
- 
-   /* try to lock file */
--  lk = HDflock(fd, LOCK_EX | LOCK_NB);
-+  lk = flock(fd, LOCK_EX | LOCK_NB);
-   
-   /* unlock so we can remove */
--  HDflock(fd, LOCK_UN);
-+  flock(fd, LOCK_UN);
-   
-   /* close */
--  HDclose(fd);
-+  close(fd);
-   
-   /* return value of lock attempt */
-   PROTECT(Rval = allocVector(INTSXP, 1));
-diff --git a/src/h5testLock.h b/src/h5testLock.h
-index 2c1c5e4..25914ff 100644
---- a/src/h5testLock.h
-+++ b/src/h5testLock.h
-@@ -1,5 +1,5 @@
- #include <fcntl.h>
-+#include <unistd.h>
- #include "myhdf5.h"
--#include <H5private.h>
- 
- SEXP _h5fileLock();

pkgs/servers/sql/postgresql/ext/plr.nix

@@ -13,13 +13,13 @@
 
 postgresqlBuildExtension (finalAttrs: {
   pname = "plr";
-  version = "8.4.8";
+  version = "8.4.8.6";
 
   src = fetchFromGitHub {
     owner = "postgres-plr";
     repo = "plr";
     tag = "REL${lib.replaceString "." "_" finalAttrs.version}";
-    hash = "sha256-FLL61HsZ6WaWBP9NqrJjhMFSVyVBIpVO0wv+kXMuAaU=";
+    hash = "sha256-SBLv9GsyYmYdxrWmGiMIiFRGl5FA+j2RcSmKz9pMv2E=";
   };
 
   nativeBuildInputs = [ pkg-config ];