diff --git a/local/backfill-flat-safety.R b/local/backfill-flat-safety.R index a8a8bbe..59faa3c 100644 --- a/local/backfill-flat-safety.R +++ b/local/backfill-flat-safety.R @@ -75,19 +75,47 @@ flat_pkg <- sub("_.*$", "", flat_files) flat_ver <- sub("\\.tar\\.gz$", "", sub("^[^_]*_", "", flat_files)) # Only compiled packages can fail at dyn.load(), so the rest are not worth -# downloading. CRAN's own index says which; it is not behind our edge. -cran <- read.dcf( - gzcon(url( - "https://cloud.r-project.org/src/contrib/PACKAGES.gz", - open = "rb" - )), - fields = c("Package", "NeedsCompilation") +# downloading. Ask the slot's own index rather than CRAN's: CRAN lists only the +# versions it currently ships, so a package it has archived is absent, is never +# recognised as compiled, and is never inspected. No verdict is ever recorded +# for it, while `union_index_records()` reads the slot's own `NeedsCompilation` +# and happily drops it -- with nothing able to clear the flag, because the +# repair works from recorded verdicts too. `mixedMem` and `vcpen`, both removed +# from CRAN, were stuck out of every rhel8 per-minor index that way. +# +# Read it from the bucket, not over HTTPS: this runs inside R, so the edge would +# route the request to a per-minor index and the flat objects would not all be +# there. Same reason the object listing above comes from S3. +index_file <- file.path(tempdir(), "flat-PACKAGES.gz") +s3fs::s3_file_download( + sprintf("%s/PACKAGES.gz", contrib), + index_file, + overwrite = TRUE ) -compiled_names <- cran[ - !is.na(cran[, "NeedsCompilation"]) & cran[, "NeedsCompilation"] == "yes", - "Package" +index <- read.dcf( + gzfile(index_file), + fields = c("Package", "Version", "NeedsCompilation") +) +if (nrow(index) == 0L) { + stop( + sprintf( + "Read no records from %s/PACKAGES.gz; refusing to guess what is compiled.", + contrib + ), + call. = FALSE + ) +} +# Key on the object, not the package: a slot can carry several versions and +# only some of them compile. +compiled_objects <- paste( + index[, "Package"], + index[, "Version"], + sep = "_" +)[ + !is.na(index[, "NeedsCompilation"]) & + tolower(index[, "NeedsCompilation"]) == "yes" ] -keep <- flat_pkg %in% compiled_names +keep <- paste(flat_pkg, flat_ver, sep = "_") %in% compiled_objects compiled <- data.frame( Package = flat_pkg[keep], Version = flat_ver[keep],