Merge pull request #221546 from NixOS/r-updates

R: 4.2.2 -> 4.2.3
2023-03-26 21:40:30 +00:00 · 2023-03-26 21:40:30 +00:00 · c39e3d9b74
commit c39e3d9b74
parent 64ccc2dccc d8d5d73bac
9 changed files with 3515 additions and 2833 deletions
--- a/pkgs/applications/science/math/R/default.nix
+++ b/pkgs/applications/science/math/R/default.nix
@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64);

 stdenv.mkDerivation (finalAttrs: {
  pname = "R";
-  version = "4.2.2";
+  version = "4.2.3";

  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-D/YrQuxRr6VxPK7nxP3noMRZQLo5vvjFyUh/7wyVPfU=";
+    sha256 = "sha256-VeSpptQ74xTiwD0CZqb6VESv3OULMDv8O4Kzl5UW4HQ=";
  };

  dontUseImakeConfigure = true;
--- a/pkgs/development/r-modules/bioc-annotation-packages.nix
+++ b/pkgs/development/r-modules/bioc-annotation-packages.nix
@ -76,10 +76,11 @@ in with self; {
  BSgenome_Hsapiens_UCSC_hg18_masked = derive2 { name="BSgenome.Hsapiens.UCSC.hg18.masked"; version="1.3.99"; sha256="031sr3y95c32igk3lrrsafdm9i1zprjran8gak06arqc0hvzbfk0"; depends=[BSgenome BSgenome_Hsapiens_UCSC_hg18]; };
  BSgenome_Hsapiens_UCSC_hg19 = derive2 { name="BSgenome.Hsapiens.UCSC.hg19"; version="1.4.3"; sha256="06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv"; depends=[BSgenome]; };
  BSgenome_Hsapiens_UCSC_hg19_masked = derive2 { name="BSgenome.Hsapiens.UCSC.hg19.masked"; version="1.3.993"; sha256="19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9"; depends=[BSgenome BSgenome_Hsapiens_UCSC_hg19]; };
-  BSgenome_Hsapiens_UCSC_hg38 = derive2 { name="BSgenome.Hsapiens.UCSC.hg38"; version="1.4.4"; sha256="03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2"; depends=[BSgenome]; };
+  BSgenome_Hsapiens_UCSC_hg38 = derive2 { name="BSgenome.Hsapiens.UCSC.hg38"; version="1.4.5"; sha256="0lp94r9dsx8sl1ifysavgjf4aamhjc4n71zif5jyfnwmzpj7g4ml"; depends=[BSgenome GenomeInfoDb]; };
  BSgenome_Hsapiens_UCSC_hg38_dbSNP151_major = derive2 { name="BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major"; version="0.0.9999"; sha256="0290fk7jvlcb1mh6nlyqagqskfh0dvaysj1d6s15bgygnlm3r726"; depends=[BSgenome]; };
  BSgenome_Hsapiens_UCSC_hg38_dbSNP151_minor = derive2 { name="BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor"; version="0.0.9999"; sha256="1xw8vckhsak35r942yyvlrpbhb2w4vzah8wfgmn3vyj1zklk3913"; depends=[BSgenome]; };
-  BSgenome_Hsapiens_UCSC_hg38_masked = derive2 { name="BSgenome.Hsapiens.UCSC.hg38.masked"; version="1.4.4"; sha256="0ac5c265pgq1yzyp655ix0awdszzxf3mhrp0qsfsb73msqb2s99n"; depends=[BSgenome BSgenome_Hsapiens_UCSC_hg38]; };
+  BSgenome_Hsapiens_UCSC_hg38_masked = derive2 { name="BSgenome.Hsapiens.UCSC.hg38.masked"; version="1.4.5"; sha256="0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m"; depends=[BSgenome BSgenome_Hsapiens_UCSC_hg38 GenomeInfoDb]; };
+  BSgenome_Hsapiens_UCSC_hs1 = derive2 { name="BSgenome.Hsapiens.UCSC.hs1"; version="1.4.4"; sha256="1y5rxlms9fj20fz32l56i5j1c4fzly5zzvlxz01fs46qimnfb3ms"; depends=[BSgenome]; };
  BSgenome_Mdomestica_UCSC_monDom5 = derive2 { name="BSgenome.Mdomestica.UCSC.monDom5"; version="1.4.2"; sha256="16kzb66kjpmf9j92pwh98ah5rhrnfyzdpr0rk659zham6dzga9ck"; depends=[BSgenome]; };
  BSgenome_Mfascicularis_NCBI_5_0 = derive2 { name="BSgenome.Mfascicularis.NCBI.5.0"; version="1.4.2"; sha256="1lrdj7aibx4i60hpbaqgk3qir9zjs67mxdgp5jmgmw7gf2nwyn3x"; depends=[BSgenome]; };
  BSgenome_Mfascicularis_NCBI_6_0 = derive2 { name="BSgenome.Mfascicularis.NCBI.6.0"; version="1.5.0"; sha256="0zl73jkg56jrvqyqvp67jx63dl8li6pypkgn1dqj959qzdzc57j0"; depends=[BSgenome]; };
@ -125,7 +126,7 @@ in with self; {
  BSgenome_Vvinifera_URGI_IGGP12Xv0 = derive2 { name="BSgenome.Vvinifera.URGI.IGGP12Xv0"; version="0.1"; sha256="1m8mqkiqs7291hccb8pfyf2yxpky45qr6j3d9wkvp9x3ra3h0yxf"; depends=[BSgenome]; };
  BSgenome_Vvinifera_URGI_IGGP12Xv2 = derive2 { name="BSgenome.Vvinifera.URGI.IGGP12Xv2"; version="0.1"; sha256="1saavsi75gw33jphhm3qb5psyfrv850ss4cmqr4i7aw1kc0fvs1j"; depends=[BSgenome]; };
  BSgenome_Vvinifera_URGI_IGGP8X = derive2 { name="BSgenome.Vvinifera.URGI.IGGP8X"; version="0.1"; sha256="0v0hi2pbbi5ynd92bvbv4bzr7bgv48kvyz62hdv7k9gh7s5pg0id"; depends=[BSgenome]; };
-  CTCF = derive2 { name="CTCF"; version="0.99.10"; sha256="0s6rscf6c4sjf6azf3blzb3lfgk7sk3clrlvmhq2gv82g9ic6d40"; depends=[]; };
+  CTCF = derive2 { name="CTCF"; version="0.99.11"; sha256="06gy1f71p01h6yfj5xmvlgz6n7sg7rpkc3723y51h30ir6xrzbrg"; depends=[]; };
  ChemmineDrugs = derive2 { name="ChemmineDrugs"; version="1.0.2"; sha256="0l47ac6lkycmghra2cbcdcxcv47ari8xg6lxpzilvkf4n6ld6064"; depends=[BiocGenerics ChemmineR RSQLite]; };
  DO_db = derive2 { name="DO.db"; version="2.9"; sha256="10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"; depends=[AnnotationDbi]; };
  ENCODExplorerData = derive2 { name="ENCODExplorerData"; version="0.99.5"; sha256="00gfm5l8pxrfs4cw4jlw6n0cz5s31isg69k833n89800v26w3kvh"; depends=[data_table jsonlite RCurl]; };
@ -219,8 +220,8 @@ in with self; {
  SNPlocs_Hsapiens_dbSNP144_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP144.GRCh38"; version="0.99.20"; sha256="0yxmsnxncr7w30r0d7bg5i96pclm2vf40p9jdqa02rc67a6sximn"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
  SNPlocs_Hsapiens_dbSNP149_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP149.GRCh38"; version="0.99.20"; sha256="17bv25p1261hn9d7mxfp6pvivj15pxyvr92gms8a8msfqg9y0xkb"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
  SNPlocs_Hsapiens_dbSNP150_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP150.GRCh38"; version="0.99.20"; sha256="0jkwwgxxpm9ry8kizq8hs70sky41pks1ag40y5aqq91yjbpqlckj"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
-  SNPlocs_Hsapiens_dbSNP155_GRCh37 = derive2 { name="SNPlocs.Hsapiens.dbSNP155.GRCh37"; version="0.99.22"; sha256="0icb85y6jc6a2rphf8dsxhfcsh7j6kmm6iii7f0dl33dsgsmb1wl"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
-  SNPlocs_Hsapiens_dbSNP155_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP155.GRCh38"; version="0.99.22"; sha256="1zdx6bjl494wlzqhhz6q6cnygbrvqimcrmmxab5dfwckkyfxlyd8"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
+  SNPlocs_Hsapiens_dbSNP155_GRCh37 = derive2 { name="SNPlocs.Hsapiens.dbSNP155.GRCh37"; version="0.99.23"; sha256="1hl63ph2j8s2igwgp0xs35a366wa7f1x6bmid09k6wqx8fcdilgy"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
+  SNPlocs_Hsapiens_dbSNP155_GRCh38 = derive2 { name="SNPlocs.Hsapiens.dbSNP155.GRCh38"; version="0.99.23"; sha256="0j4skfz6g7ir1igqbql0hk04871vpfqg7dpmvv9z6k2mx9lnrh7w"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; };
  TxDb_Athaliana_BioMart_plantsmart22 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart22"; version="3.0.1"; sha256="0j2zr4cddad7z1lxx9m9kfgyy7jajjnblpk9j8igd39ia3ixrpzc"; depends=[AnnotationDbi GenomicFeatures]; };
  TxDb_Athaliana_BioMart_plantsmart25 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart25"; version="3.1.3"; sha256="0a6v0l6p13zmiysi3k8dxzdlxng552qqj9rnlbdavdiidla0pvm3"; depends=[AnnotationDbi GenomicFeatures]; };
  TxDb_Athaliana_BioMart_plantsmart28 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart28"; version="3.2.2"; sha256="1yjyvrbx55y024lqg3b2rlf8pngqw5xi3p83j5ipan05wf0aq6ir"; depends=[AnnotationDbi GenomicFeatures]; };
--- a/pkgs/development/r-modules/bioc-experiment-packages.nix
+++ b/pkgs/development/r-modules/bioc-experiment-packages.nix
@ -22,7 +22,7 @@ in with self; {
  BeadArrayUseCases = derive2 { name="BeadArrayUseCases"; version="1.36.0"; sha256="079qj26622s9jb2kw1wpd5bjihmj3a9mif4y86zjna7jm1jdvzv8"; depends=[beadarray GEOquery limma]; };
  BeadSorted_Saliva_EPIC = derive2 { name="BeadSorted.Saliva.EPIC"; version="1.6.0"; sha256="0mh10sg95djkzp9w7bjr4ggy86a0pakfi2008fk4xikjc3q7ky24"; depends=[ExperimentHub minfi]; };
  BioImageDbs = derive2 { name="BioImageDbs"; version="1.6.0"; sha256="0r4m5qchzglpx4dn95ss0xfd3cqd7vxafjg869y8fxpayjn11dqg"; depends=[animation AnnotationHub EBImage einsum ExperimentHub filesstrings magick magrittr markdown rmarkdown]; };
-  BioPlex = derive2 { name="BioPlex"; version="1.4.2"; sha256="091d9gywkkbgd922sgqqqnj20sjnrsarqrhqbw99x9ccnfzqr2jn"; depends=[BiocFileCache GenomeInfoDb GenomicRanges GEOquery graph SummarizedExperiment]; };
+  BioPlex = derive2 { name="BioPlex"; version="1.4.3"; sha256="01kal3fg1ii6cx33ccar3aaq36a11irg1ac8fcanm5xr4lhsf8v8"; depends=[BiocFileCache GenomeInfoDb GenomicRanges GEOquery graph SummarizedExperiment]; };
  BloodCancerMultiOmics2017 = derive2 { name="BloodCancerMultiOmics2017"; version="1.18.0"; sha256="1284qhij9663b382aq4nq3zl3jjsj5gdh3bfqj6sjfvbvx4pmcpg"; depends=[beeswarm Biobase DESeq2 devtools dplyr ggdendro ggplot2 glmnet gtable ipflasso RColorBrewer reshape2 scales SummarizedExperiment survival tibble]; };
  CCl4 = derive2 { name="CCl4"; version="1.36.0"; sha256="09zja5jzz7lh11cyjvczfgic8z4bq35j6f63irwwizxvp861w902"; depends=[Biobase limma]; };
  CLL = derive2 { name="CLL"; version="1.38.0"; sha256="109sspddzqg08gqf5xacf2vbjs672i2d3n6a6wzr8isdyar40xx1"; depends=[affy Biobase]; };
@ -131,7 +131,7 @@ in with self; {
  MethylSeqData = derive2 { name="MethylSeqData"; version="1.8.0"; sha256="0rfl5xz23kbvjxf2sf25j526a8252dvd6zmg4x9pj7fqyf7yvfdd"; depends=[ExperimentHub GenomeInfoDb GenomicRanges HDF5Array IRanges rhdf5 S4Vectors SummarizedExperiment]; };
  MicrobiomeBenchmarkData = derive2 { name="MicrobiomeBenchmarkData"; version="1.0.0"; sha256="06m0yi3379g8kvhs0amcc9r5d0np9xwq2a85vk8iz3xi6sqbbbzj"; depends=[ape BiocFileCache S4Vectors SummarizedExperiment TreeSummarizedExperiment]; };
  MouseGastrulationData = derive2 { name="MouseGastrulationData"; version="1.12.0"; sha256="0icgs53mfaiary8gjifasjalc9942fr876w61bxssdg7v4jn76ss"; depends=[BiocGenerics BumpyMatrix ExperimentHub S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
-  MouseThymusAgeing = derive2 { name="MouseThymusAgeing"; version="1.6.0"; sha256="0y5xibhd5w37ks3fvn6gsgqd5whxvg1rbd4li2ank0v56mvazfij"; depends=[BiocGenerics ExperimentHub S4Vectors SingleCellExperiment SummarizedExperiment]; };
+  MouseThymusAgeing = derive2 { name="MouseThymusAgeing"; version="1.6.1"; sha256="11hs19zcpa8bfmidm7v9hll735c6waq37s879mwz4wgxw9ysk1nl"; depends=[BiocGenerics ExperimentHub S4Vectors SingleCellExperiment SummarizedExperiment]; };
  NCIgraphData = derive2 { name="NCIgraphData"; version="1.34.0"; sha256="0sismlawhq1dz29v1532x5ha1n2pdv2fa43kzma4xdf1vafj5ham"; depends=[]; };
  NGScopyData = derive2 { name="NGScopyData"; version="1.18.0"; sha256="1w3hpmqf6030smwb4r61czwz0qsr2kz8z11q8z8819bj0czvr32x"; depends=[]; };
  NanoporeRNASeq = derive2 { name="NanoporeRNASeq"; version="1.8.0"; sha256="0k548ib7yi29xcs2c0y46c3vwi6fkqsp3njwbn4acm85pr93z54g"; depends=[ExperimentHub]; };
@ -222,7 +222,7 @@ in with self; {
  VectraPolarisData = derive2 { name="VectraPolarisData"; version="1.2.0"; sha256="0gl92bypw6axdwj83dxmvib7p72dl1n5vqfrsy398fahx24djwln"; depends=[ExperimentHub SpatialExperiment]; };
  WES_1KG_WUGSC = derive2 { name="WES.1KG.WUGSC"; version="1.30.0"; sha256="0yi72kdihvrxf7w72fn24bs5r89pg10kc9myl8n4nmf2iiplcn0c"; depends=[]; };
  WGSmapp = derive2 { name="WGSmapp"; version="1.10.0"; sha256="0lgfmpmnwpmrg05nz8vxlkz3jwy6gkd74fl7a2f81bh2lrs4bgh1"; depends=[GenomicRanges]; };
-  WeberDivechaLCdata = derive2 { name="WeberDivechaLCdata"; version="1.0.0"; sha256="1zqc26n7945b024ln82yqp5zpsmb7d5bi8zgj8hqnm09bna3qiil"; depends=[ExperimentHub SingleCellExperiment SpatialExperiment]; };
+  WeberDivechaLCdata = derive2 { name="WeberDivechaLCdata"; version="1.0.1"; sha256="1swdzlcja42adx4j5h82nskbks8lkhbq07gvb9p09q2lg8rylc7q"; depends=[ExperimentHub SingleCellExperiment SpatialExperiment]; };
  XhybCasneuf = derive2 { name="XhybCasneuf"; version="1.36.0"; sha256="1r09wr45vjcr7yxxfi5l132bqg380bicdlz699961hbinvyg7pgc"; depends=[affy ath1121501cdf RColorBrewer tinesath1cdf]; };
  adductData = derive2 { name="adductData"; version="1.14.0"; sha256="0yfgjvq7qk5gvdjhrh2lyz77c6jd438ykd2mpfm6643zr2bkxp4g"; depends=[AnnotationHub ExperimentHub]; };
  affycompData = derive2 { name="affycompData"; version="1.36.0"; sha256="0qcjlm2i0z8z6ab7dknwl1pdmxv69hyfpj61lhygn8ks02al12kn"; depends=[affycomp Biobase]; };
@ -269,10 +269,10 @@ in with self; {
  curatedBladderData = derive2 { name="curatedBladderData"; version="1.34.0"; sha256="1vp9w40v37xgjdsg8m0w7580h2i0xi823f34qik87mj1hr5xawsf"; depends=[affy]; };
  curatedBreastData = derive2 { name="curatedBreastData"; version="2.26.0"; sha256="02iflnwfpcmglj060w5zygqccii91n2s0vp9bkl1ppj6g409pxm3"; depends=[Biobase BiocStyle ggplot2 impute XML]; };
  curatedCRCData = derive2 { name="curatedCRCData"; version="2.30.0"; sha256="0hbc3d1sj1mfqszmfgkmhpnkbw4mdapp85s7bj2spmcwf0pcsr0n"; depends=[BiocGenerics nlme]; };
-  curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.6.0"; sha256="0ry9063nmcc5n289a2h7rpv7dgf25i3yk44nfsslfy73bvrdnz75"; depends=[AnnotationHub dplyr ExperimentHub magrittr mia purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
+  curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.6.2"; sha256="1qlsjif43pjsm7gkxlvixgpd457q9jgj3ikmvxan4wi6hfw4rxwi"; depends=[AnnotationHub dplyr ExperimentHub magrittr mia purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
  curatedOvarianData = derive2 { name="curatedOvarianData"; version="1.36.0"; sha256="09zb3m32a2rqwgs2x6g1ixvwnbx0100mb2m8rkbkdlfczlnq9riq"; depends=[affy BiocGenerics]; };
  curatedTBData = derive2 { name="curatedTBData"; version="1.4.0"; sha256="0ksb30h6hlksxzgp0dl1f09jr4a59zdll9jnla8xcsbqqvbkm4g7"; depends=[AnnotationHub ExperimentHub MultiAssayExperiment rlang]; };
-  curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.20.0"; sha256="01q3bcspvff2syg5d933iqfxwl62axfy4xbzkwlg15as7bl7a54r"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
+  curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.20.1"; sha256="0w3iv044gynhb90bis58dz6znh2fgy7zdgs1yyjzx4fphxzg32j6"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
  davidTiling = derive2 { name="davidTiling"; version="1.38.0"; sha256="1g8q0m03ss7nf2v3rk6db93mmbzy1kc960scs37pc3s9xdm7k9ak"; depends=[Biobase GO_db tilingArray]; };
  depmap = derive2 { name="depmap"; version="1.12.0"; sha256="10y1s5v6c74ynq8m0rck41w16hglnr700c322k5p9yzndf86f3hv"; depends=[AnnotationHub dplyr ExperimentHub]; };
  derfinderData = derive2 { name="derfinderData"; version="2.16.0"; sha256="147bf7x90prw1x58gy6w13l02sf6zbn4888ikw817k9n5ja3f3x1"; depends=[]; };
--- a/pkgs/development/r-modules/bioc-packages.nix
+++ b/pkgs/development/r-modules/bioc-packages.nix
--- a/pkgs/development/r-modules/cran-packages.nix
+++ b/pkgs/development/r-modules/cran-packages.nix
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@ -389,7 +389,7 @@ let
    Rglpk = [ pkgs.glpk ];
    RGtk2 = [ pkgs.gtk2.dev ];
    rhdf5 = [ pkgs.zlib ];
-    Rhdf5lib = with pkgs; [ zlib.dev hdf5.dev ];
+    Rhdf5lib = with pkgs; [ zlib.dev ];
    Rhpc = with pkgs; [ zlib bzip2.dev icu xz.dev mpi pcre.dev ];
    Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ];
    rjags = [ pkgs.jags ];
@ -582,7 +582,7 @@ let
    podkat = [ pkgs.zlib.dev ];
    qrqc = [ pkgs.zlib.dev ];
    rJPSGCS = [ pkgs.zlib.dev ];
-    rhdf5filters = [ pkgs.zlib.dev ];
+    rhdf5filters = with pkgs; [ zlib.dev bzip2.dev ];
    rtk = [ pkgs.zlib.dev ];
    scPipe = [ pkgs.zlib.dev ];
    seqTools = [ pkgs.zlib.dev ];
@ -970,6 +970,10 @@ let
      preConfigure = "patchShebangs configure";
    });

+    purrr = old.purrr.overrideAttrs (attrs: {
+      patchPhase = "patchShebangs configure";
+    });
+
    RcppArmadillo = old.RcppArmadillo.overrideAttrs (attrs: {
      patchPhase = "patchShebangs configure";
    });
@ -1315,8 +1319,21 @@ let
      RGL_USE_NULL = "true";
    });

-    Rhdf5lib = old.Rhdf5lib.overrideAttrs (attrs: {
-      propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.hdf5.dev ];
+    Rhdf5lib = let
+      hdf5 = pkgs.hdf5_1_10.overrideAttrs (attrs: {configureFlags = attrs.configureFlags ++ ["--enable-cxx"];});
+    in old.Rhdf5lib.overrideAttrs (attrs: {
+      propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ hdf5.dev pkgs.libaec ];
+      patches = [ ./patches/Rhdf5lib.patch ];
+      passthru.hdf5 = hdf5;
+    });
+
+    rhdf5filters = old.rhdf5filters.overrideAttrs (attrs: {
+      propagatedBuildInputs = with pkgs; attrs.propagatedBuildInputs ++ [ (hdf5-blosc.override {hdf5 = self.Rhdf5lib.hdf5;}) ];
+      patches = [ ./patches/rhdf5filters.patch ];
+    });
+
+    rhdf5= old.rhdf5.overrideAttrs (attrs: {
+      patches = [ ./patches/rhdf5.patch ];
    });
  };
 in
--- a/pkgs/development/r-modules/patches/Rhdf5lib.patch
+++ b/pkgs/development/r-modules/patches/Rhdf5lib.patch
@ -0,0 +1,79 @@
+diff --git a/R/zzz.R b/R/zzz.R
+index 97becd7..803ca39 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", "
+ 
+   path <- Sys.getenv(
+     x = "RHDF5LIB_RPATH",
+-    unset = system.file("lib", package="Rhdf5lib", mustWork=TRUE)
+    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',
+                                       patharch, winlibs)
+                             }, {
+-                              sprintf('"%s/libhdf5.a"%s%s', 
+                              sprintf('-lhdf5',
+                                       patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                             }
+                      )
+@@ -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',
+                                       patharch, winlibs)
+                             }, {
+-                              sprintf('"%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
+                              sprintf('-lhdf5_cpp -lhdf5',
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                             }
+                      )
+@@ -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',
+                                       patharch, winlibs)
+                             }, {
+-                              sprintf('"%s/libhdf5_hl.a" "%s/libhdf5.a"%s%s', 
+                              sprintf('-lhdf5_hl -lhdf5',
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                             }
+                      )
+@@ -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',
+                                       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())
+                             }
+                      )
+@@ -124,6 +124,7 @@ getHdf5Version <- function() {
+ #'
+ #' @keywords internal
+ .getDynamicLinks <- function() {
+  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}"
--- a/pkgs/development/r-modules/patches/rhdf5.patch
+++ b/pkgs/development/r-modules/patches/rhdf5.patch
@ -0,0 +1,46 @@
+diff --git a/src/Makevars b/src/Makevars
+index 713b44c..704ac17 100644
+--- a/src/Makevars
+++ b/src/Makevars
+@@ -1,5 +1,5 @@
+ RHDF5_LIBS = $(shell "$(R_HOME)/bin${R_ARCH_BIN}/Rscript" -e 'Rhdf5lib::pkgconfig("PKG_C_LIBS")')
+-PKG_LIBS = $(RHDF5_LIBS)
+PKG_LIBS = $(RHDF5_LIBS) -lhdf5
+ 
+ #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..660c747 100644
+--- a/src/h5testLock.h
+++ b/src/h5testLock.h
+@@ -1,5 +1,4 @@
+ #include <fcntl.h>
+ #include "myhdf5.h"
+-#include <H5private.h>
+ 
+ SEXP _h5fileLock();
--- a/pkgs/development/r-modules/patches/rhdf5filters.patch
+++ b/pkgs/development/r-modules/patches/rhdf5filters.patch
@ -0,0 +1,46 @@
+diff --git a/src/Makevars.in b/src/Makevars.in
+index 4441634..665a2dd 100644
+--- a/src/Makevars.in
+++ b/src/Makevars.in
+@@ -20,10 +20,9 @@ export PKG_LDFLAGS=@LDFLAGS@
+ all: copying $(SHLIB)
+ 
+ #copy hdf5 library headers to package include
+-copying: blosc/libH5Zblosc.so bzip2/libH5Zbz2.so lzf/libH5Zlzf.so
+copying: bzip2/libH5Zbz2.so lzf/libH5Zlzf.so
+ 	mkdir -p "${USER_LIB_DIR}"
+ 	cp ${BZIP2_LIB} "${USER_LIB_DIR}"
+-	cp ${BLOSC_LIB} "${USER_LIB_DIR}"
+ 	cp ${LZF_LIB} "${USER_LIB_DIR}"
+ 
+ blosc/libH5Zblosc.so:
+diff --git a/src/bzip2/Makefile b/src/bzip2/Makefile
+index 449bbe7..154354e 100644
+--- a/src/bzip2/Makefile
+++ b/src/bzip2/Makefile
+@@ -1,9 +1,9 @@
+ 
+ all: libH5Zbz2.so
+ 
+-libH5Zbz2.so: bzip2-1.0.8/libbz2.a
+-	${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zbzip2.c $(PKG_CPPFLAGS) \
+-	-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a ${PKG_LDFLAGS} -o libH5Zbz2.so
+libH5Zbz2.so:
+	${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zbzip2.c \
+	   -lbz2 -o libH5Zbz2.so
+ 
+ bzip2-1.0.8/libbz2.a:
+ 	$(MAKE) -C bzip2-1.0.8
+diff --git a/src/lzf/Makefile b/src/lzf/Makefile
+index 837f80b..eeca0c8 100644
+--- a/src/lzf/Makefile
+++ b/src/lzf/Makefile
+@@ -2,7 +2,7 @@
+ all: libH5Zlzf.so
+ 
+ libH5Zlzf.so: lzf/liblzf.a
+-	${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zlzf.c $(PKG_CPPFLAGS) \
+	${CC} ${PKG_CFLAGS} ${PKG_CPICFLAGS} -shared H5Zlzf.c \
+ 	-I./lzf/ ./lzf/liblzf.a ${PKG_LDFLAGS} -o libH5Zlzf.so
+ 
+ lzf/liblzf.a: