r-modules: use HTTPS, allow passing args from generated set, use MRAN
This commit is contained in:
Nikolay Amiantov
Peter Simons
parent
5ee5b5ba82
commit
287f99bada
@ -300,120 +300,15 @@ rec {
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# The commented-out ones don't seem to allow direct package downloads;
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# they serve error messages that result in hash mismatches instead.
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bioc = [
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# http://bioc.ism.ac.jp/3.2/bioc/
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# http://bioc.openanalytics.eu/3.2/bioc/
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# http://bioconductor.fmrp.usp.br/3.2/bioc/
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# http://mirror.aarnet.edu.au/pub/bioconductor/3.2/bioc/
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# http://watson.nci.nih.gov/bioc_mirror/3.2/bioc/
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http://bioconductor.jp/packages/3.2/bioc/
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http://bioconductor.statistik.tu-dortmund.de/packages/3.2/bioc/
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http://mirrors.ebi.ac.uk/bioconductor/packages/3.2/bioc/
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http://mirrors.ustc.edu.cn/bioc/3.2/bioc/
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];
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# CRAN mirrors (from http://cran.r-project.org/mirrors.html)
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cran = [
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http://cran.r-project.org/
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http://cran.rstudio.com/
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http://cran.usthb.dz/
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http://mirror.fcaglp.unlp.edu.ar/CRAN/
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http://cran.csiro.au/
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http://cran.ms.unimelb.edu.au/
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http://cran.at.r-project.org/
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http://www.freestatistics.org/cran/
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http://nbcgib.uesc.br/mirrors/cran/
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http://cran-r.c3sl.ufpr.br/
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http://cran.fiocruz.br/
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http://www.vps.fmvz.usp.br/CRAN/
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http://brieger.esalq.usp.br/CRAN/
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http://cran.stat.sfu.ca/
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http://mirror.its.dal.ca/cran/
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http://cran.utstat.utoronto.ca/
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http://cran.skazkaforyou.com/
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http://cran.parentingamerica.com/
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http://dirichlet.mat.puc.cl/
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http://ftp.ctex.org/mirrors/CRAN/
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http://mirror.bjtu.edu.cn/cran
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http://mirrors.ustc.edu.cn/CRAN/
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http://mirrors.xmu.edu.cn/CRAN/
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http://www.laqee.unal.edu.co/CRAN/
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http://www.icesi.edu.co/CRAN/
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http://mirrors.nic.cz/R/
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http://mirrors.dotsrc.org/cran/
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http://cran.espol.edu.ec/
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http://cran.salud.gob.sv/
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http://ftp.eenet.ee/pub/cran/
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http://cran.univ-lyon1.fr/
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http://mirror.ibcp.fr/pub/CRAN/
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http://ftp.igh.cnrs.fr/pub/CRAN/
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http://cran.irsn.fr/
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http://cran.univ-paris1.fr/
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http://cran.cardse.net/
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http://mirrors.softliste.de/cran/
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http://ftp5.gwdg.de/pub/misc/cran/
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http://cran.sciserv.eu/
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http://cran.uni-muenster.de/
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http://cran.cc.uoc.gr/mirrors/CRAN/
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http://cran.rapporter.net/
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http://cran.hafro.is/
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http://ftp.iitm.ac.in/cran/
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http://cran.repo.bppt.go.id/
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http://cran.um.ac.ir/
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http://ftp.heanet.ie/mirrors/cran.r-project.org/
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http://cran.mirror.garr.it/mirrors/CRAN/
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http://cran.stat.unipd.it/
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http://dssm.unipa.it/CRAN/
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http://cran.ism.ac.jp/
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http://cran.md.tsukuba.ac.jp/
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http://cran.nexr.com/
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http://healthstat.snu.ac.kr/CRAN/
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http://cran.biodisk.org/
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http://rmirror.lau.edu.lb/
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http://cran.itam.mx/
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http://www.est.colpos.mx/R-mirror/
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http://cran.xl-mirror.nl/
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http://cran-mirror.cs.uu.nl/
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http://cran.stat.auckland.ac.nz/
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http://cran.uib.no/
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http://cran.stat.upd.edu.ph/
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http://r.meteo.uni.wroc.pl/
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http://cran.dcc.fc.up.pt/
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http://cran.gis-lab.info/
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http://cran.stat.nus.edu.sg/
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http://cran.fyxm.net/
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http://r.adu.org.za/
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http://cran.mirror.ac.za/
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http://ftp.cixug.es/CRAN/
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http://cran.es.r-project.org/
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http://ftp.sunet.se/pub/lang/CRAN/
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http://stat.ethz.ch/CRAN/
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http://ftp.yzu.edu.tw/CRAN/
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http://cran.csie.ntu.edu.tw/
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http://mirrors.psu.ac.th/pub/cran/
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http://cran.pau.edu.tr/
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http://www.stats.bris.ac.uk/R/
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http://mirrors.ebi.ac.uk/CRAN/
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http://cran.ma.imperial.ac.uk/
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http://mirror.mdx.ac.uk/R/
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http://star-www.st-andrews.ac.uk/cran/
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http://cran.cnr.berkeley.edu/
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http://cran.stat.ucla.edu/
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http://streaming.stat.iastate.edu/CRAN/
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http://ftp.ussg.iu.edu/CRAN/
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http://rweb.quant.ku.edu/cran/
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http://watson.nci.nih.gov/cran_mirror/
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http://cran.mtu.edu/
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http://cran.wustl.edu/
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http://cran.case.edu/
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http://ftp.osuosl.org/pub/cran/
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http://lib.stat.cmu.edu/R/CRAN/
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http://cran.mirrors.hoobly.com/
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http://mirrors.nics.utk.edu/cran/
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http://cran.revolutionanalytics.com/
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http://cran.fhcrc.org/
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http://cran.cs.wwu.edu/
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http://camoruco.ing.uc.edu.ve/cran/
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http://cran.vinastat.com/
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# http://bioc.ism.ac.jp/
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# http://bioc.openanalytics.eu/
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# http://bioconductor.fmrp.usp.br/
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# http://mirror.aarnet.edu.au/pub/bioconductor/
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# http://watson.nci.nih.gov/bioc_mirror/
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http://bioconductor.jp/packages/
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http://bioconductor.statistik.tu-dortmund.de/packages/
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http://mirrors.ebi.ac.uk/bioconductor/packages/
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http://mirrors.ustc.edu.cn/bioc/
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];
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# Hackage mirrors
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@ -11,7 +11,10 @@ let
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#
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# some packages, e.g. cncaGUI, require X running while installation,
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# so that we use xvfb-run if requireX is true.
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mkDerive = {mkHomepage, mkUrls}: lib.makeOverridable ({
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mkDerive = {mkHomepage, mkUrls}: args:
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# XXX: not ideal ("2.2" would match "2.22") but sufficient
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assert (!(args ? rVersion) || lib.hasPrefix args.rVersion (lib.getVersion R));
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lib.makeOverridable ({
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name, version, sha256,
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depends ? [],
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doCheck ? true,
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@ -22,12 +25,12 @@ let
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name = "${name}-${version}";
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src = fetchurl {
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inherit sha256;
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urls = mkUrls { inherit name version; };
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urls = mkUrls (args // { inherit name version; });
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};
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inherit doCheck requireX;
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propagatedBuildInputs = depends;
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nativeBuildInputs = depends;
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meta.homepage = mkHomepage name;
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meta.homepage = mkHomepage (args // { inherit name; });
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meta.platforms = R.meta.platforms;
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meta.hydraPlatforms = hydraPlatforms;
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meta.broken = broken;
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@ -37,18 +40,15 @@ let
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# from the name, version, sha256, and optional per-package arguments above
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#
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deriveBioc = mkDerive {
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mkHomepage = name: "http://cran.r-project.org/web/packages/${name}/";
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mkUrls = {name, version}: [ "mirror://bioc/src/contrib/${name}_${version}.tar.gz" ];
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mkHomepage = {name, rVersion}: "https://bioconductor.org/packages/${rVersion}/bioc/html/${name}.html";
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mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/bioc/src/contrib/${name}_${version}.tar.gz" ];
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};
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deriveCran = mkDerive {
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mkHomepage = name: "http://bioconductor.org/packages/release/bioc/html/${name}.html";
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mkUrls = {name, version}: [
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"mirror://cran/src/contrib/${name}_${version}.tar.gz"
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"mirror://cran/src/contrib/00Archive/${name}/${name}_${version}.tar.gz"
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];
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mkHomepage = {name, snapshot}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/";
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mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ];
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};
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deriveIRkernel = mkDerive {
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mkHomepage = name: "http://irkernel.github.io/";
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mkHomepage = {name}: "https://irkernel.github.io/";
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mkUrls = {name, version}: [ "http://irkernel.github.io/src/contrib/${name}_${version}.tar.gz" ];
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};
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@ -7,14 +7,16 @@ mirrorType <- commandArgs(trailingOnly=TRUE)[1]
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stopifnot(mirrorType %in% c("bioc","cran", "irkernel"))
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packagesFile <- paste(mirrorType, 'packages.nix', sep='-')
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readFormatted <- as.data.table(read.table(skip=6, sep='"', text=head(readLines(packagesFile), -1)))
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readFormatted <- as.data.table(read.table(skip=8, sep='"', text=head(readLines(packagesFile), -1)))
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rVersion <- paste(R.Version()$major, strsplit(R.Version()$minor, ".", fixed=TRUE)[[1]][1], sep=".")
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snapshotDate <- Sys.Date()
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mirrorUrls <- list( bioc="http://bioconductor.statistik.tu-dortmund.de/packages/3.2/bioc/src/contrib/"
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, cran="http://cran.r-project.org/src/contrib/"
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, irkernel="http://irkernel.github.io/src/contrib/"
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mirrorUrls <- list( bioc=paste0("https://bioconductor.statistik.tu-dortmund.de/packages/", rVersion, "/bioc/src/contrib/")
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, cran=paste0("https://mran.revolutionanalytics.com/snapshot/", snapshotDate, "/src/contrib/")
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, irkernel="https://irkernel.github.io/src/contrib/"
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)
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mirrorUrl <- mirrorUrls[mirrorType][[1]]
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knownPackages <- lapply(mirrorUrls, function(url) as.data.table(available.packages(url, filters=c("R_version", "OS_type", "duplicates"))))
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knownPackages <- lapply(mirrorUrls, function(url) as.data.table(available.packages(url, filters=c("R_version", "OS_type", "duplicates")), method="libcurl"))
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pkgs <- knownPackages[mirrorType][[1]]
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setkey(pkgs, Package)
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knownPackages <- c(unique(do.call("rbind", knownPackages)$Package))
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@ -38,12 +40,12 @@ formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
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depends <- sapply(depends, gsub, pattern=".", replacement="_", fixed=TRUE)
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depends <- depends[depends %in% knownPackages]
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depends <- paste(sort(unique(depends)), collapse=" ")
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paste0(attr, " = derive { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
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paste0(" ", attr, " = derive2 { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
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}
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clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "knownPackages"))
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pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates")))
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pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates"), method="libcurl"))
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pkgs <- pkgs[order(Package)]
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pkgs$sha256 <- parApply(cl, pkgs, 1, function(p) nixPrefetch(p[1], p[2]))
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@ -54,8 +56,14 @@ cat("# Execute the following command to update the file.\n")
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cat("#\n")
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cat(paste("# Rscript generate-r-packages.R", mirrorType, ">new && mv new", packagesFile))
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cat("\n\n")
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cat("{ self, derive }: with self; {\n")
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cat(paste(nix, collapse="\n"), "\n")
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cat("{ self, derive }:\n")
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cat("let derive2 = derive ")
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if (mirrorType == "bioc") { cat("{ rVersion = \"", rVersion, "\"; }", sep="")
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} else if (mirrorType == "cran") { cat("{ snapshot = \"", paste(snapshotDate), "\"; }", sep="")
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} else if (mirrorType == "irkernel") { cat("{}") }
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cat(";\n")
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cat("in with self; {\n")
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cat(paste(nix, collapse="\n"), "\n", sep="")
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cat("}\n")
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stopCluster(cl)
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16
pkgs/development/r-modules/generate-shell.nix
Normal file
16
pkgs/development/r-modules/generate-shell.nix
Normal file
@ -0,0 +1,16 @@
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with import <nixpkgs> {};
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stdenv.mkDerivation {
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name = "generate-r-packages-shell";
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buildCommand = "exit 1";
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nativeBuildInputs = [
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(rWrapper.override {
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packages = with rPackages; [
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data_table
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parallel
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];
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})
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];
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}
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