pat-s
8a98cf96a6
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s3fs uses reticulate/Python which significantly increases R process memory. When pak tries to fork R to install package dependencies, the enlarged process can't be duplicated within the container memory limit. Now the install-deps step saves the S3 file listing as s3_cache.rds, and the build step reads it with readRDS() — no s3fs loading needed.
72 lines
2.9 KiB
R
72 lines
2.9 KiB
R
sink(stdout(), type = "message")
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options(crayon.enabled = TRUE, future.globals.onReference = NULL)
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args <- commandArgs(trailingOnly = TRUE)
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split_into <- as.integer(args[1])
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split_index <- as.integer(args[2])
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ncpus <- as.integer(args[3])
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options(Ncpus = ncpus)
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# Load bincraft eagerly to avoid lazy-load memory spike during first build call
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library(bincraft, quietly = TRUE)
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library(future)
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plan("sequential")
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# Read precomputed package+version pairs
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pkgs <- readRDS("/mnt/cache/packages/pkgs_to_build.rds")
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sprintf("Total# of remaining package versions: %s", nrow(pkgs))
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# Split into chunks for this worker
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chunks <- split(pkgs, cut(seq_len(nrow(pkgs)), split_into, labels = FALSE))
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chunk <- chunks[[split_index]]
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sprintf("# of package versions for this job: %s", nrow(chunk))
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# Exclude known problematic packages
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exclude <- c(
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"RInno", "KeyboardSimulator", "R2PPT", "RWinEdt", "blatr", "excel.link",
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"spectrino", "taskscheduleR", "MDSGUI", "BiplotGUI", "R2wd", "rFUSION",
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"MediaNews", "doBy", "IDPmisc", "frailtypack", "afex", "FrF2", "DoE.base",
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"agricolae", "doFuture", "fscaret", "PHYLOGR", "seewave", "pls", "relaimpo",
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"geepack", "gggenes", "NPCirc", "repmis", "PNDSIBGE", "lidR", "poismf",
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"neonstore", "MachineShop", "mvst", "MacBehaviour", "mcmcderive", "RGIFT",
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"KnowBR", "netmeta", "spdep", "Rfast", "compareGroups", "ff", "GsymPoint",
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"RcppDynProg", "comtradr", "FD", "PearsonDS", "DCluster", "gRc", "mixlm",
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"geospt", "fdth", "ffmanova", "fiery", "ffscrapr", "cold",
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"RcmdrPlugin.DoE", "RcmdrPlugin.NMBU", "RcmdrPlugin.RiskDemo",
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"RcmdrPlugin.ROC", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos",
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"RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.aRnova",
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"RcmdrPlugin.depthTools", "RcmdrPlugin.orloca", "RcmdrPlugin.sos",
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"RcmdrPlugin.survival", "RcmdrPlugin.temis", "GWlasso", "GWmodelVis"
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)
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chunk <- chunk[!chunk$Package %in% exclude, ]
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# Read pre-computed S3 listing from install-deps step
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# This avoids loading s3fs/reticulate/Python in the build container,
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# saving significant memory for pak subprocess forks
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s3_cache <- readRDS("/mnt/cache/packages/s3_cache.rds")
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sprintf("S3 cache: %s files", length(s3_cache))
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n <- nrow(chunk)
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mapply(function(pkg, ver, i) {
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cat(sprintf("[%d/%d] %s_%s\n", i, n, pkg, ver))
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bincraft::build_binary_package(
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pkg,
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tag = ver,
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s3_endpoint = "https://s3.eu-central-003.backblazeb2.com",
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s3_region = "eu-central-003",
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s3_bucket = "devxy-rpkgs-binaries",
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s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"),
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s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"),
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s3_package_cache = s3_cache,
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metadata_db_host = "r-binaries.devxy.io",
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metadata_db_name = "build_metadata",
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metadata_db_table = "single_builds",
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metadata_db_user = "rpkgs",
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metadata_db_password = Sys.getenv("PGPASS"),
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metadata_db_sslmode = "require",
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metadata_db_port = 15432,
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archive = TRUE,
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upload = TRUE,
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store_build_metadata = TRUE
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)
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}, chunk$Package, chunk$Version, seq_len(n))
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