[r/ci] R CI fails today with "Error in readRDS(dest) : error reading from connection"

[johnkerl]

R CI has a persistent fail this morning on multiple PRs (I don't believe it to be due to anything we've changed) -- example

https://github.com/single-cell-data/TileDB-SOMA/actions/runs/11744407390/job/32719440280

[1] "methods"   "Rcpp"      "nanotime"  "spdl"      "nanoarrow" "RcppInt64"
Error in readRDS(dest) : error reading from connection
Calls: <Anonymous> ... eval -> eval -> <Anonymous> -> <Anonymous> -> readRDS

[sc-59087]

Docker repro

$ alias dreb
alias dreb='docker run --rm -it --entrypoint=/bin/bash'

$ dreb eddelbuettel/r2u:jammy

# apt-get update
# apt-get install -y git cmake

# cd /tmp
# git clone https://github.com/single-cell-data/TileDB-SOMA
# cd TileDB-SOMA

Then follow lines from our r-ci.yml:

# cd apis/r

# tools/r-ci.sh bootstrap

Then run these in R:

rversion <- paste(strsplit(as.character(getRversion()), split = '\\.')[[1L]][1:2], collapse = '.')
codename <-  system('. /etc/os-release; echo ${VERSION_CODENAME}', intern = TRUE)
repo <- "https://tiledb-inc.r-universe.dev"
(opt <- sprintf('options(repos = c("%s/bin/linux/%s/%s", "%s", getOption("repos")), timeout = 300L)', repo, codename, rversion, repo))
cat(opt, "\n", file = "~/.Rprofile", append = TRUE)

Then

# Rscript tools/install-tiledb-r.R

  comp   vers
1   >= 0.30.0
[1] "methods"   "Rcpp"      "nanotime"  "spdl"      "nanoarrow" "RcppInt64"
Error in readRDS(dest) : error reading from connection
Calls: <Anonymous> ... eval -> eval -> <Anonymous> -> <Anonymous> -> readRDS
Execution halted

In an R session so I can get a traceback:

>
> source('tools/install-tiledb-r.R')
Error in readRDS(dest) : error reading from connection
> traceback()
12: readRDS(dest)
11: utils::available.packages(contriburl = contriburl, method = method,
        ...)
10: (utils::getFromNamespace("install_both", asNamespace("bspm")))(pkgs,
        contriburl, method, dependencies, ...)
9: eval(expr, p)
8: eval(expr, p)
7: eval.parent(exprObj)
6: .doTrace({
       if (missing(pkgs))
           stop("no packages were specified")
       if (type == "both" && !getOption("bspm.version.check", TRUE))
           type <- "binary-source"
       if (is.null(repos)) {
           type <- "source"
       }
       else if (type == "both") {
           pkgs <- (utils::getFromNamespace("install_both", asNamespace("bspm")))(pkgs,
               contriburl, method, dependencies, ...)
           type <- "source"
       }
       else if (type == "binary") {
           if (!length(pkgs <- bspm::install_sys(pkgs)))
               type <- "source"
       }
       else if (type == "binary-source") {
           type <- "both"
           pkgs <- (utils::getFromNamespace("install_fast", asNamespace("bspm")))(pkgs,
               contriburl, method, ...)
           type <- "source"
       }
   })
5: utils::install.packages(intersect(ups, rownames(db))) at install-tiledb-r.R#48
4: eval(ei, envir)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("tools/install-tiledb-r.R")

[johnkerl]

Running lines from tools/install-tiledb.R interactively:

> utils::install.packages(intersect(ups, rownames(db)))
Error in readRDS(dest) : error reading from connection

> intersect(ups, rownames(db))
[1] "Rcpp"      "nanotime"  "spdl"      "nanoarrow" "RcppInt64"

> utils::install.packages('Rcpp')
Error in readRDS(dest) : error reading from connection
> utils::install.packages('nanotime')
Error in readRDS(dest) : error reading from connection
> utils::install.packages('spdl')
Error in readRDS(dest) : error reading from connection
> utils::install.packages('nanoarrow')
Error in readRDS(dest) : error reading from connection
> utils::install.packages('RcppInt64')
Error in readRDS(dest) : error reading from connection

[johnkerl]

When I comment out the .Rprofile line

options(repos = c("https://tiledb-inc.r-universe.dev/bin/linux/jammy/4.4", "https://tiledb-inc.r-universe.dev", getOption("repos")), timeout = 300L)

then the tools/install-tiledb-r.R runs successfully

[johnkerl]

A re-run of https://github.com/single-cell-data/TileDB-SOMA/actions/runs/11745810131/job/32724737665 is now not failing ...

[johnkerl]

https://github.com/single-cell-data/TileDB-SOMA/actions/runs/11745810131/job/32724737665 just ran to completion.

Problem appears to have been transient.

cc @mojaveazure

[johnkerl]

@mojaveazure has some follow-up thoughts which he understands well; re-assigning