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R updates (#523821)

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This commit is contained in:
Justin Bedő
2026-06-06 13:16:27 +00:00
committed by GitHub
parent 4bb2f933a7 476399fb33
commit 00fa9a692b
9 changed files with 21068 additions and 15152 deletions
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pkgs/applications/science/math/R/default.nix
+2 -2
View File
@@ -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
+33 -33
View File
@@ -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/bioc-experiment-packages.json
+946 -911
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pkgs/development/r-modules/bioc-packages.json
+5493 -4938
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File diff suppressed because it is too large Load Diff
pkgs/development/r-modules/cran-packages.json
+14517 -9180
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File diff suppressed because it is too large Load Diff
pkgs/development/r-modules/default.nix
+52 -5
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@@ -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 $dev/lib
'';
});
in
old.Rhdf5lib.overrideAttrs (attrs: {
propagatedBuildInputs = attrs.propagatedBuildInputs ++ [
pkgs/development/r-modules/patches/Rhdf5lib.patch
+23 -45
View File
@@ -1,8 +1,8 @@
diff --git a/R/zzz.R b/R/zzz.R
index 97becd7..803ca39 100644
index 2af2b3e..21ddc00 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -20,7 +20,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
@@ -22,7 +22,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
path <- Sys.getenv(
x = "RHDF5LIB_RPATH",
@@ -10,70 +10,48 @@ index 97becd7..803ca39 100644
+ unset = ""
)
if (nzchar(.Platform$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
-36
View File
@@ -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
+2 -2
View File
@@ -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 ];