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R,rPackages: 4.4.2 -> 4.4.3 (#385925)

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This commit is contained in:
Justin Bedő
2025-03-14 10:24:33 +11:00
committed by GitHub
parent fdfc4347e9 6c745acde8
commit 3b9548edf8
5 changed files with 7258 additions and 4961 deletions
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pkgs/applications/science/math/R/default.nix
+2 -2
View File
@@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64);
stdenv.mkDerivation (finalAttrs: {
pname = "R";
version = "4.4.2";
version = "4.4.3";
src = let
inherit (finalAttrs) pname version;
in fetchurl {
url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
sha256 = "sha256-FXjNYD6NhmtYdD5J2L+ZxWnoEHm2pgzzPN973/64F+w=";
sha256 = "sha256-DZPSJEQt6iU8KwhvCI220NPP2bWSzVSW6MshQ+kPyeg=";
};
outputs = [ "out" "tex" ];
pkgs/development/r-modules/bioc-experiment-packages.json
+18 -18
View File
@@ -749,9 +749,9 @@
},
"MetaScope": {
"name": "MetaScope",
"version": "1.5.4",
"sha256": "1f69bkm7qb027pl1c1w9vlvbcw0sxi0da5az21a8i8xrz42aab57",
"depends": ["BiocFileCache", "Biostrings", "Matrix", "MultiAssayExperiment", "Rbowtie2", "Rsamtools", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "ggplot2", "magrittr", "readr", "rlang", "stringr", "tibble", "tidyr"]
"version": "1.6.0",
"sha256": "1f7w4dfv6sizpp97vjwm034ha4pcq93b3j0gg1l75s6ans8s89aw",
"depends": ["BiocFileCache", "Biostrings", "Matrix", "MultiAssayExperiment", "Rbowtie2", "Rsamtools", "S4Vectors", "SummarizedExperiment", "data_table", "dplyr", "ggplot2", "magrittr", "readr", "rlang", "stringr", "taxize", "tibble", "tidyr"]
},
"MethylAidData": {
"name": "MethylAidData",
@@ -1139,8 +1139,8 @@
},
"STexampleData": {
"name": "STexampleData",
"version": "1.14.0",
"sha256": "1n2cq1ia7vi7a2gma9mhwv34dwy0fyxmap5fycy3f8f2bnm373kw",
"version": "1.14.1",
"sha256": "14xdinp0ix55lgs0adcxwnjascrpx4s39kghrhbcpjl0ainrdhk3",
"depends": ["ExperimentHub", "SingleCellExperiment", "SpatialExperiment"]
},
"SVM2CRMdata": {
@@ -1319,9 +1319,9 @@
},
"TumourMethData": {
"name": "TumourMethData",
"version": "1.3.0",
"sha256": "01xbsi6x4bafkp0m5xi4l2w62067xnfqnlkaz59ng1hf2ld2p690",
"depends": ["ExperimentHub", "GenomicRanges", "HDF5Array", "R_utils", "SummarizedExperiment", "rhdf5"]
"version": "1.4.0",
"sha256": "14y58qa4khi4jdymilxrb6x57br1gjclw2q3n9mivjrj6z3r3nmw",
"depends": ["BSgenome_Hsapiens_UCSC_hg19", "ExperimentHub", "ExperimentHubData", "GenomicRanges", "HDF5Array", "R_utils", "SummarizedExperiment", "TCGAutils", "dplyr", "knitr", "methrix", "openxlsx", "readr", "rhdf5", "rmarkdown", "stringr", "tibble", "usethis", "xlsx"]
},
"VariantToolsData": {
"name": "VariantToolsData",
@@ -1739,9 +1739,9 @@
},
"etec16s": {
"name": "etec16s",
"version": "1.33.0",
"sha256": "1xbj8z68006riah51lpk0bh8hq240wl9n1inlss84yj6kn4y5m0w",
"depends": ["Biobase"]
"version": "1.34.0",
"sha256": "114jmrnjm2xpfzx1m10bn73fy1am209c70ws4jwfggrbavg6xp8j",
"depends": ["Biobase", "metagenomeSeq"]
},
"ewceData": {
"name": "ewceData",
@@ -1817,8 +1817,8 @@
},
"gDRtestData": {
"name": "gDRtestData",
"version": "1.4.0",
"sha256": "1qqk9x8i2g5284p60hxznl95b6sp80qksx4qq724ycmknayg3kxb",
"version": "1.4.1",
"sha256": "0ybp2zrkjivrfl62zz7jljs1inlnx3iybwazyh0rxb255r9cg9ns",
"depends": ["checkmate", "data_table"]
},
"gageData": {
@@ -2117,9 +2117,9 @@
},
"msd16s": {
"name": "msd16s",
"version": "1.25.0",
"sha256": "0lzcpwf9rhr8i80hn3dab0fpgx7qmy0q9l8j7fkrazq2paiiikj7",
"depends": ["Biobase"]
"version": "1.26.0",
"sha256": "0wg705d0232d4916d3b84q62pdrzmf8v3k9apyh4fsmg4pk2xw6p",
"depends": ["Biobase", "metagenomeSeq"]
},
"msdata": {
"name": "msdata",
@@ -2207,8 +2207,8 @@
},
"pRolocdata": {
"name": "pRolocdata",
"version": "1.44.0",
"sha256": "0dh5zgwr248gnlygja7ly66dyhh4b4xf72n9ycp0xa02xdl0mwi3",
"version": "1.44.1",
"sha256": "01n9p4a02lq96rhz97skzs79mvnki3vqyn3b4b89vhrp8idgmli0",
"depends": ["Biobase", "MSnbase"]
},
"parathyroidSE": {
pkgs/development/r-modules/bioc-packages.json
+226 -238
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pkgs/development/r-modules/cran-packages.json
+6876 -4681
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pkgs/development/r-modules/default.nix
+136 -22
View File
@@ -370,11 +370,12 @@ let
diversitree = with pkgs; [ gsl fftw ];
exactextractr = [ pkgs.geos ];
EMCluster = [ pkgs.lapack ];
fangs = [ pkgs.cargo ];
fangs = with pkgs; [ cargo rustc ];
fastpng = [ pkgs.zlib.dev ];
fcl = with pkgs; [ cargo rustc ];
fftw = [ pkgs.fftw.dev ];
fftwtools = with pkgs; [ fftw.dev pkg-config ];
flint = with pkgs; [ pkg-config gmp.dev mpfr.dev flint3 ];
fingerPro = [ pkgs.gsl ];
Formula = [ pkgs.gmp ];
frailtyMMpen = [ pkgs.gsl ];
@@ -401,6 +402,7 @@ let
RNiftyReg = with pkgs; [ zlib.dev ];
highs = [ pkgs.which pkgs.cmake ];
crc32c = [ pkgs.which pkgs.cmake ];
cpp11bigwig = with pkgs; [ zlib.dev curl.dev ];
rbedrock = [ pkgs.zlib.dev pkgs.which pkgs.cmake ];
HiCseg = [ pkgs.gsl ];
imager = [ pkgs.xorg.libX11.dev ];
@@ -450,6 +452,7 @@ let
PKI = [ pkgs.openssl.dev ];
png = [ pkgs.libpng.dev ];
protolite = [ pkgs.protobuf ];
prqlr = with pkgs; [ cargo rustc ];
R2SWF = with pkgs; [ zlib libpng freetype.dev ];
RAppArmor = [ pkgs.libapparmor ];
rapportools = [ pkgs.which ];
@@ -495,9 +498,9 @@ let
httpuv = [ pkgs.zlib.dev ];
clustermq = [ pkgs.zeromq ];
SAVE = with pkgs; [ zlib bzip2 icu xz pcre ];
salso = [ pkgs.cargo ];
salso = with pkgs; [ cargo rustc ];
ymd = with pkgs; [ cargo rustc ];
arcpbf = [ pkgs.cargo ];
arcpbf = with pkgs; [ cargo rustc ];
sdcTable = with pkgs; [ gmp glpk ];
seewave = with pkgs; [ fftw.dev libsndfile.dev ];
seqinr = [ pkgs.zlib.dev ];
@@ -513,6 +516,7 @@ let
arcgisutils = with pkgs; [ cargo rustc ];
arcgisgeocode = with pkgs; [ cargo rustc ];
arcgisplaces = with pkgs; [ pkg-config openssl.dev cargo rustc ];
awdb = [ pkgs.cargo ];
apcf = with pkgs; [ geos ];
SemiCompRisks = [ pkgs.gsl ];
showtext = with pkgs; [ zlib libpng icu freetype.dev ];
@@ -521,6 +525,7 @@ let
ssanv = [ pkgs.proj ];
stsm = [ pkgs.gsl ];
stringi = [ pkgs.icu.dev ];
parseLatex = [ pkgs.icu.dev ];
survSNP = [ pkgs.gsl ];
svglite = [ pkgs.libpng.dev ];
sysfonts = with pkgs; [ zlib libpng freetype.dev ];
@@ -588,6 +593,7 @@ let
rrd = [ pkgs.pkg-config ];
surveyvoi = [ pkgs.pkg-config ];
Rbwa = [ pkgs.zlib.dev ];
tergo = with pkgs; [ cargo rustc ];
trackViewer = [ pkgs.zlib.dev ];
themetagenomics = [ pkgs.zlib.dev ];
Rsymphony = [ pkgs.pkg-config ];
@@ -599,9 +605,11 @@ let
qqconf = [ pkgs.pkg-config ];
qspray = [ pkgs.pkg-config ];
ratioOfQsprays = [ pkgs.pkg-config ];
watcher = with pkgs; [ cmake which ];
symbolicQspray = [ pkgs.pkg-config ];
sphereTessellation = [ pkgs.pkg-config ];
vapour = [ pkgs.pkg-config ];
xdvir = [ pkgs.freetype.dev ];
};
packagesWithBuildInputs = {
@@ -908,6 +916,7 @@ let
"MSnID"
"OmnipathR"
"orthGS"
"pannotator"
"precommit"
"protGear"
"PCRA"
@@ -982,6 +991,7 @@ let
"HierO"
"HIBAG"
"HiveR"
"minired" # deprecated on CRAN
# Impure network access during build
"waddR"
@@ -1016,6 +1026,17 @@ let
];
otherOverrides = old: new: {
ACME = old.ACME.overrideAttrs (attrs: {
env = (attrs.env or { }) // {
# Avoid incompatible pointer type error
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-incompatible-pointer-types";
};
});
vegan3d = old.vegan3d.overrideAttrs (attrs: {
RGL_USE_NULL = "true";
});
# it can happen that the major version of arrow-cpp is ahead of the
# rPackages.arrow that would be built from CRAN sources; therefore, to avoid
# build failures and manual updates of the hash, we use the R source at
@@ -1025,11 +1046,6 @@ let
# this is a straightforward approach. Example where patching was necessary
# -> arrow 14.0.0.2 on CRAN; was lagging behind libarrow release:
# https://github.com/apache/arrow/issues/39698 )
vegan3d = old.vegan3d.overrideAttrs (attrs: {
RGL_USE_NULL = "true";
});
arrow = old.arrow.overrideAttrs (attrs: {
src = pkgs.arrow-cpp.src;
name = "r-arrow-${pkgs.arrow-cpp.version}";
@@ -1058,6 +1074,14 @@ let
];
});
gmapR = old.gmapR.overrideAttrs (attrs: {
env = (attrs.env or { }) // {
# Avoid incompatible pointer type error
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE +
" -Wno-implicit-function-declaration -Wno-incompatible-pointer-types";
};
});
timeless = old.timeless.overrideAttrs (attrs: {
preConfigure = "patchShebangs configure";
cargoDeps = pkgs.rustPlatform.fetchCargoVendor {
@@ -1074,6 +1098,10 @@ let
];
});
arcpbf = old.arcpbf.overrideAttrs (attrs: {
postPatch = "patchShebangs configure";
});
stringi = old.stringi.overrideAttrs (attrs: {
postInstall = let
icuName = "icudt52l";
@@ -1095,18 +1123,51 @@ let
'';
});
findpython = old.findpython.overrideAttrs (attrs: {
postPatch = ''
substituteInPlace "R/find_python_cmd.r" \
--replace-fail 'python_cmds[which(python_cmds != "")]' \
'python_cmds <- c(python_cmds, file.path("${lib.getBin pkgs.python3}", "bin", "python3"))
python_cmds[which(python_cmds != "")]'
'';
});
alcyon = old.alcyon.overrideAttrs (attrs: {
configureFlags = [
"--enable-force-openmp"
];
});
awdb = old.awdb.overrideAttrs (attrs: {
postPatch = ''
patchShebangs configure
'';
});
clarabel = old.clarabel.overrideAttrs (attrs: {
postPatch = ''
patchShebangs configure
'';
});
lwgeom = old.lwgeom.overrideAttrs (attrs: {
configureFlags = [
"--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib"
];
});
scDDboost = old.scDDboost.overrideAttrs (attrs: {
postPatch = ''
# https://code.bioconductor.org/browse/scDDboost/commit/f704a727c906075a2e271e9e2db93cf31e3822f5
substituteInPlace "DESCRIPTION" \
--replace-fail "c++11" "c++14"
# https://code.bioconductor.org/browse/scDDboost/commit/74d46e266957b38fe77185fa3ce683f891706538
substituteInPlace "src/Makevars" \
--replace-fail "#CXX_STD = CXX11" "CXX_STD = CXX14"
'';
});
sf = old.sf.overrideAttrs (attrs: {
configureFlags = [
"--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib"
@@ -1129,6 +1190,10 @@ let
preConfigure = "patchShebangs configure";
});
nanoparquet = old.nanoparquet.overrideAttrs (attrs: {
postPatch = "patchShebangs configure";
});
clustermq = old.clustermq.overrideAttrs (attrs: {
preConfigure = "patchShebangs configure";
});
@@ -1161,10 +1226,25 @@ let
postPatch = "patchShebangs configure";
});
EBSeq = old.EBSeq.overrideAttrs (attrs: {
postPatch = ''
# https://code.bioconductor.org/browse/EBSeq/commit/d18c41cc3eb96ca82a7c55f0d60287e28785281e
substituteInPlace "DESCRIPTION" \
--replace-fail "c++11" "c++14"
# https://code.bioconductor.org/browse/EBSeq/commit/fd9ccf425b3c8c0f209de77e7d6e9a1d0c839d68
substituteInPlace "src/Makevars" \
--replace-fail "#CXX_STD = CXX11" "CXX_STD = CXX14"
'';
});
gmailr = old.gmailr.overrideAttrs (attrs: {
postPatch = "patchShebangs configure";
});
prqlr = old.prqlr.overrideAttrs (attrs: {
postPatch = "patchShebangs configure";
});
pingr = old.pingr.overrideAttrs (_: {
postPatch = "patchShebangs configure";
});
@@ -1216,6 +1296,21 @@ let
postPatch = "patchShebangs configure";
});
bandle = old.bandle.overrideAttrs (attrs: {
postPatch = ''
# https://code.bioconductor.org/browse/bandle/commit/e8f7aaa29c1ba772cee5d51e09b1f500bfee44b8
substituteInPlace "src/Makevars" \
--replace-fail "CXX_STD = CXX11" "CXX_STD = CXX14"
'';
});
graper = old.graper.overrideAttrs (attrs: {
postPatch = ''
substituteInPlace "src/Makevars" \
--replace-fail "CXX_STD=CXX11" "CXX_STD=CXX14"
'';
});
ocf = old.ocf.overrideAttrs (attrs: {
postPatch = "patchShebangs configure";
});
@@ -1279,6 +1374,14 @@ let
'';
});
metahdep = old.metahdep.overrideAttrs (attrs: {
env = (attrs.env or { }) // {
# Avoid incompatible pointer type error
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-int-conversion";
};
});
ModelMetrics = old.ModelMetrics.overrideAttrs (attrs: {
env = (attrs.env or { }) // {
NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.hostPlatform.isDarwin " -fopenmp";
@@ -1566,6 +1669,21 @@ let
buildInputs = [ cacert ] ++ attrs.buildInputs;
});
float = old.float.overrideAttrs (attrs: {
enableParallelBuilding = false;
});
redatamx = old.redatamx.overrideAttrs (attrs: {
preConfigure = let
redatam-core = pkgs.fetchzip {
url = "https://redatam-core.s3.us-west-2.amazonaws.com/core-dev/linux/redatamx-core-linux-20241222.zip";
hash = "sha256-CagDpv7v5fj/NgaC5fmYc5UuKuBVlT3gauH2ItVnIIY=";
};
in ''
mkdir -p ./inst/redengine/
cp ${redatam-core}/lib/libredengine-1.0.0-rc2.so ./inst/redengine/libredengine-1.0.0-rc2.so
'';
});
immunotation = let
MHC41alleleList = fetchurl {
@@ -1779,6 +1897,16 @@ let
RGL_USE_NULL = "true";
});
methylKit = old.methylKit.overrideAttrs (attrs: {
# resolve missing function from data.table
patches = [
(pkgs.fetchpatch {
url = "https://github.com/al2na/methylKit/commit/5c30347630bc064d7aefc918923f723671f35253.patch";
sha256 = "sha256-hwtybBmSYwVInMIEZ7i7zudJWjiRJmrD0/tU7v78pPc=";
})
];
});
Rrdrand = old.Rrdrand.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
symengine = old.symengine.overrideAttrs (_: {
@@ -1799,20 +1927,6 @@ let
postPatch = "patchShebangs configure";
});
SharedObject = old.SharedObject.overrideAttrs (attrs: {
# backport PR resolving build issues: https://github.com/Jiefei-Wang/SharedObject/pull/17
patches = let inherit (pkgs) fetchpatch; in [
(fetchpatch {
url = "https://github.com/Jiefei-Wang/SharedObject/pull/17/commits/50c4b2964649d7f5a14d843bd7089ab62650fcd3.patch";
sha256 = "sha256-zn535IeOYRvyQ2yxgoGEq2wccrl9xdu9nREmy7sV+PQ=";
})
(fetchpatch {
url = "https://github.com/Jiefei-Wang/SharedObject/pull/17/commits/bf096a39858e9210cbe246d4b136905d4cfbfaf4.patch";
sha256 = "sha256-Z+BZOkFnLgIBiVuPsAHp7bMXzADcvuHV4hILdmLvd+k=";
})
];
});
httr2 = old.httr2.overrideAttrs (attrs: {
preConfigure = "patchShebangs configure";
});