Last updated on 2026-06-08 13:50:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.6.2 | 70.65 | 514.79 | 585.44 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.6.2 | 48.80 | 303.41 | 352.21 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.6.2 | 115.00 | 795.47 | 910.47 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.6.2 | 125.00 | 696.36 | 821.36 | OK | |
| r-devel-windows-x86_64 | 0.6.2 | 79.00 | 495.00 | 574.00 | OK | |
| r-patched-linux-x86_64 | 0.6.2 | 67.91 | 495.03 | 562.94 | OK | |
| r-release-linux-x86_64 | 0.6.2 | 67.58 | 490.46 | 558.04 | OK | |
| r-release-macos-arm64 | 0.6.2 | 13.00 | 104.00 | 117.00 | OK | |
| r-release-macos-x86_64 | 0.6.2 | 39.00 | 463.00 | 502.00 | OK | |
| r-release-windows-x86_64 | 0.6.2 | 78.00 | 496.00 | 574.00 | OK | |
| r-oldrel-macos-arm64 | 0.6.2 | 13.00 | 104.00 | 117.00 | OK | |
| r-oldrel-macos-x86_64 | 0.6.2 | 46.00 | 690.00 | 736.00 | OK | |
| r-oldrel-windows-x86_64 | 0.6.2 | 97.00 | 687.00 | 784.00 | OK |
Version: 0.6.2
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [53s/330s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(bamm)
>
> test_check("bamm")
Set A of the BAM digram it contains 8 slots
@niche_model: a niche model:
class : RasterLayer
dimensions : 91, 159, 14469 (nrow, ncol, ncell)
resolution : 0.2, 0.2 (x, y)
extent : -118.4042, -86.60417, 14.51846, 32.71846 (xmin, xmax, ymin, ymax)
crs : +proj=longlat +datum=WGS84 +no_defs
source : memory
names : layer
values : 0, 1 (min, max)
@suit_threshold: Threshold value used to binarize model@cellIDs: ids of the cells that have values (4281 pixels)
@suit_values: Suitability values of the continuous model
@sparse_model: A sparse square matrix of 4281 x 4281 entries
@coordinates: Pixel centroid coordinates of the model
Set M of the BAM digram it contains 7 slots
@coordinates: A matrix with longitude and latitude values of each cell of the raster area
x y
[1,] -115.9042 32.61846
[2,] -115.7042 32.61846
[3,] -115.5042 32.61846
[4,] -115.3042 32.61846
[5,] -115.1042 32.61846
[6,] -114.9042 32.61846
@eigen_val: Eigen values of the connectivity matrix M
@eigen_vec: Eigen vector of the connectivity matrix M
Object of class csd it contains 3 slots:
@connections: Geographic clusters data.frame
x y clusterID cluster_size
1 -116.3042 32.41846 1 37
2 -116.7042 32.21846 1 37
3 -116.5042 32.21846 1 37
4 -116.3042 32.21846 1 37
@interactive_map: A leaflet map showing the geographic clusters
@raster_map: A raster map of the clusters
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|======================================================================| 100%Set M of the BAM digram it contains 7 slots
@coordinates: A matrix with longitude and latitude values of each cell of the raster area
x y
[1,] -115.9042 32.61846
[2,] -115.7042 32.61846
[3,] -115.5042 32.61846
[4,] -115.3042 32.61846
[5,] -115.1042 32.61846
[6,] -114.9042 32.61846
@eigen_val: Eigen values of the connectivity matrix M
[1] 7.975459
@eigen_vec: Eigen vector of the connectivity matrix M
[,1]
[1,] -8.640620e-11
[2,] -1.555028e-10
[3,] -2.564191e-10
[4,] -4.169028e-10
[5,] -6.556495e-10
[6,] -8.733471e-10
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|======================================================================| 100%Object of class pam it contains 5 slots:
@pams: A list of sparse PAM matrices
6 x 7 sparse Matrix of class "dgCMatrix"
x y
77 -91.66667 82.66667 . . . . .
78 -90.66667 82.66667 . . . . .
79 -89.66667 82.66667 . . . . .
80 -88.66667 82.66667 . . . . .
81 -87.66667 82.66667 . . . . .
82 -86.66667 82.66667 . . . . .
@sp_names: the species in the pam with 5 species:
Brachylagus_idahoensis, Lepus_alleni, Lepus_americanus, Lepus_arcticus, Lepus_californicus
@which_steps: time steps 1 2 3 4 5 6 7 8 9 10
@grid: raster grid of the studied area
class : RasterLayer
dimensions : 75, 112, 8400 (nrow, ncol, ncell)
resolution : 1, 1 (x, y)
extent : -168.1667, -56.16667, 8.166667, 83.16667 (xmin, xmax, ymin, ymax)
crs : +proj=longlat +datum=WGS84 +no_defs
source : memory
names : layer
values : 0, 1 (min, max)
@cellIDs: site ids regarding the raster grid
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Saving _problems/test-bam-474.R
New names:
* `dfield` -> `dfield...1`
* `dfield` -> `dfield...2`
* `dfield` -> `dfield...3`
* `dfield` -> `dfield...4`
* `dfield` -> `dfield...5`
* `dfield` -> `dfield...6`
* `dfield` -> `dfield...7`
* `dfield` -> `dfield...8`
* `dfield` -> `dfield...9`
* `dfield` -> `dfield...10`
This function uses the code from:
https://github.com/zpneal/fastball/blob/main/fastball.cpp
Please when using the function for publications cite:
Godard K, Neal ZP (2022). 'fastball: a fast algorithm to randomly
sample bipartite graphs with fixed degree sequences'.
Journal of Complex Networks, 10(6), cnac049.
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Progress: ──────────────────────────────────────────────────────────────── 100%New names:
* `dfield` -> `dfield...1`
* `dfield` -> `dfield...2`
* `dfield` -> `dfield...3`
* `dfield` -> `dfield...4`
* `dfield` -> `dfield...5`
* `dfield` -> `dfield...6`
* `dfield` -> `dfield...7`
* `dfield` -> `dfield...8`
* `dfield` -> `dfield...9`
* `dfield` -> `dfield...10`
This function uses the code from:
https://github.com/zpneal/fastball/blob/main/fastball.cpp
Please when using the function for publications cite:
Godard K, Neal ZP (2022). 'fastball: a fast algorithm to randomly
sample bipartite graphs with fixed degree sequences'.
Journal of Complex Networks, 10(6), cnac049.
Object of class bioindex it contains 8 slots:
@alpha: A sparse matrix with the richness of species per site
<S4 Type Object>
attr(,"Dim")
[1] 10 1
attr(,"Dimnames")
attr(,"Dimnames")[[1]]
NULL
attr(,"Dimnames")[[2]]
NULL
attr(,"x")
[1] 2 3 0 1 4 1 1 5 3 5
attr(,"factors")
list()
attr(,"class")
[1] "dgeMatrix"
attr(,"class")attr(,"package")
[1] "Matrix"
@omega: A sparse matrix with the range size of every species
<S4 Type Object>
attr(,"Dim")
[1] 10 1
attr(,"Dimnames")
attr(,"Dimnames")[[1]]
NULL
attr(,"Dimnames")[[2]]
NULL
attr(,"x")
[1] 1 1 2 3 3 3 1 3 3 5
attr(,"factors")
list()
attr(,"class")
[1] "dgeMatrix"
attr(,"class")attr(,"package")
[1] "Matrix"
@dispersion_field: A sparse with the set of ranges of all species that occur in at each locality
<S4 Type Object>
attr(,"Dim")
[1] 10 1
attr(,"Dimnames")
attr(,"Dimnames")[[1]]
NULL
attr(,"Dimnames")[[2]]
NULL
attr(,"x")
[1] 1 1 2 3 3 3 1 3 3 5
attr(,"factors")
list()
attr(,"class")
[1] "dgeMatrix"
attr(,"class")attr(,"package")
[1] "Matrix"
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|======================================================================| 100%Output at: /tmp/RtmpkQf51T/anima_2793b9450002b.gif
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 62 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-bam.R:194:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bam.R:473:3'): community_sim simulates community dynamics and returns an
object of class ──
Error in `(function (workers, makeNode = makeNodePSOCK, port = c("auto", "random"), user = NULL, ..., autoStop = FALSE, tries = getOption2("parallelly.makeNodePSOCK.tries", 3L), delay = getOption2("parallelly.makeNodePSOCK.tries.delay", 15), validate = getOption2("parallelly.makeNodePSOCK.validate", TRUE), verbose = isTRUE(getOption("parallelly.debug"))) { if (verbose) { verbose_prefix <- "[local output] " oopts <- options(parallelly.debug = verbose) mdebugf_push("%smakeClusterPSOCK() ...", verbose_prefix) on.exit({ mdebugf_pop("%smakeClusterPSOCK() ... done", verbose_prefix) options(oopts) }) } localhostHostname <- getOption2("parallelly.localhost.hostname", "localhost") if (is.numeric(workers)) { if (length(workers) != 1L) { stopf("When numeric, argument 'workers' must be a single value: %s", length(workers)) } workers <- structure(as.integer(workers), class = class(workers)) if (is.na(workers) || workers < 1L) { stopf("Number of 'workers' must be one or greater: %s", workers) } checkNumberOfLocalWorkers(workers) workers <- rep(localhostHostname, times = workers) } if (!is.null(user)) { stop_if_not(is.character(user), length(user) == 1L || length(user) == length(workers)) user <- rep(user, length.out = length(workers)) } tries <- as.integer(tries) stop_if_not(length(tries) == 1L, is.integer(tries), !is.na(tries), tries >= 1L) delay <- as.numeric(delay) stop_if_not(length(delay) == 1L, is.numeric(delay), !is.na(delay), delay >= 0) validate <- as.logical(validate) stop_if_not(length(validate) == 1L, is.logical(validate), !is.na(validate)) if (identical(makeNode, makeNodePSOCK)) { free <- freeConnections() if (validate) free <- free - 1L if (length(workers) > free) { msg <- sprintf("Cannot create %d parallel PSOCK nodes. Each node needs one connection, but there are only %d connections left out of the maximum %d available on this R installation", length(workers), free, availableConnections()) if (getRversion() >= "4.4.0") { msg <- sprintf("%s. To increase this limit in R (>= 4.4.0), use command-line option '--max-connections=N' when launching R", msg) } hint <- detectCoresHint(length(workers)) if (!is.null(hint)) msg <- sprintf("%s. %s", msg, hint) stopf(msg) } } if (verbose) { mdebugf("%sWorkers: [n = %d] %s", verbose_prefix, length(workers), hpaste(sQuote(workers))) } if (length(port) == 0L) { stop("Argument 'port' must be of length one or more: 0") } port_org <- port port <- freePort(port) if (verbose) mdebugf("%sBase port: %d", verbose_prefix, port) if (is.na(port)) { stop("Argument 'port' specifies non-available port(s): ", paste(port_org, collapse = ", ")) } n <- length(workers) nodeOptions <- vector("list", length = n) if (verbose) mdebugf("%sGetting setup options for %d cluster nodes ...", verbose_prefix, n) for (ii in seq_len(n)) { if (verbose) mdebugf("%sNode #%d of %d ...", verbose_prefix, ii, n) user_ii <- user[ii] if (!is.null(user_ii) && user_ii == "*") user_ii <- NULL options <- makeNode(workers[[ii]], port = port, user = user_ii, ..., rank = ii, action = "options", verbose = verbose) stop_if_not(inherits(options, "makeNodePSOCKOptions")) nodeOptions[[ii]] <- options } if (verbose) mdebugf("%sGetting setup options for %d cluster nodes ... done", verbose_prefix, n) setup_strategy <- lapply(nodeOptions, FUN = function(options) { value <- options$setup_strategy if (is.null(value)) value <- "sequential" stop_if_not(is.character(value), length(value) == 1L) value }) setup_strategy <- unlist(setup_strategy, use.names = FALSE) is_parallel <- (setup_strategy == "parallel") force_sequential <- FALSE if (any(is_parallel)) { if (verbose) mdebugf("%sParallel setup requested for some PSOCK nodes", verbose_prefix) if (!all(is_parallel)) { if (verbose) mdebugf("%sParallel setup requested only for some PSOCK nodes; will revert to a sequential setup for all", verbose_prefix) force_sequential <- TRUE } else { affected <- affected_by_bug18119() if (!is.na(affected) && affected) { if (verbose) mdebugf("%sParallel setup requested but not supported on this version of R: %s", verbose_prefix, getRversion()) force_sequential <- TRUE } } } if (force_sequential) { setup_strategy <- "sequential" for (ii in which(is_parallel)) { if (verbose) mdebugf("%sNode #%d of %d ...", verbose_prefix, ii, n) user_ii <- user[ii] if (!is.null(user_ii) && user_ii == "*") user_ii <- NULL args <- list(workers[[ii]], port = port, user = user_ii, ..., rank = ii, action = "options", verbose = verbose) args$setup_strategy <- "sequential" options <- do.call(makeNode, args = args) stop_if_not(inherits(options, "makeNodePSOCKOptions")) nodeOptions[[ii]] <- options } } stopifnot(length(nodeOptions) == n) setup_strategy <- lapply(nodeOptions, FUN = function(options) { value <- options$setup_strategy if (is.null(value)) value <- "sequential" stop_if_not(is.character(value), length(value) == 1L) value }) stopifnot(length(setup_strategy) == n) setup_strategy <- unlist(setup_strategy, use.names = FALSE) setup_strategy <- unique(setup_strategy) stop_if_not(length(setup_strategy) == 1L) cl <- vector("list", length = length(nodeOptions)) class(cl) <- c("RichSOCKcluster", "SOCKcluster", "cluster") stopifnot(length(cl) == length(nodeOptions)) on.exit({ nodes <- vapply(cl, FUN = inherits, c("SOCKnode", "SOCK0node"), FUN.VALUE = FALSE) stopCluster(cl[nodes]) cl <- NULL }, add = TRUE) if (setup_strategy == "parallel") { if (getRversion() < "4.0.0") { stopf("Parallel setup of PSOCK cluster nodes is not supported in R %s", getRversion()) socketAccept <- serverSocket <- function(...) NULL } sendCall <- importParallel("sendCall") recvResult <- importParallel("recvResult") options <- nodeOptions[[1]] if (verbose) { mdebugf("%sSetting up PSOCK nodes in parallel", verbose_prefix) mstr(options) } port <- options[["port"]] connectTimeout <- options[["connectTimeout"]] timeout <- options[["timeout"]] useXDR <- options[["useXDR"]] nodeClass <- c("RichSOCKnode", if (useXDR) "SOCKnode" else "SOCK0node") cmd <- options[["cmd"]] if (verbose) { mdebugf("%sSystem call to launch all workers:", verbose_prefix) mdebugf("%s%s", verbose_prefix, cmd) } if (verbose) mdebugf("%sStarting PSOCK main server", verbose_prefix) socket <- serverSocket(port = port) on.exit(if (!is.null(socket)) close(socket), add = TRUE) assert_system_is_supported() if (.Platform[["OS.type"]] == "windows") { for (ii in seq_along(cl)) { system(cmd, wait = FALSE, input = "") } } else { cmd <- paste(rep(cmd, times = length(cl)), collapse = " & ") system(cmd, wait = FALSE) } if (verbose) mdebugf("%sWorkers launched", verbose_prefix) ready <- 0L pending <- list() on.exit({ lapply(pending, FUN = function(x) close(x$con)) cl <- NULL }, add = TRUE) if (verbose) mdebugf_push("%sWaiting for workers to connect back ...", verbose_prefix) t0 <- Sys.time() while (ready < length(cl)) { if (verbose) mdebugf("%s%d workers out of %d ready", verbose_prefix, ready, length(cl)) cons <- lapply(pending, FUN = function(x) x$con) if (difftime(Sys.time(), t0, units = "secs") > connectTimeout + 5) { failed <- length(cl) - ready stop(sprintf(ngettext(failed, "Cluster setup failed (connectTimeout=%.1f seconds). %d worker of %d failed to connect.", "Cluster setup failed (connectTimeout=%.1f seconds). %d of %d workers failed to connect."), connectTimeout + 5, failed, length(cl))) } a <- socketSelect(append(list(socket), cons), write = FALSE, timeout = connectTimeout) canAccept <- a[1] canReceive <- seq_along(pending)[a[-1]] if (canAccept) { attr(localhostHostname, "localhost") <- TRUE con <- socketAccept(socket = socket, blocking = TRUE, open = "a+b", timeout = timeout) options$rank <- ready options$pidfile <- NULL scon <- structure(list(con = con, host = localhostHostname, rank = ready), options = options, calls = sys.calls(), class = nodeClass) res <- tryCatch({ sendCall(scon, eval, list(quote(Sys.getpid()))) }, error = identity) pending <- append(pending, list(scon)) } for (scon in pending[canReceive]) { pid <- tryCatch({ recvResult(scon) }, error = identity) if (is.integer(pid)) { ready <- ready + 1L cl[[ready]] <- scon } else { close(scon$con) } } if (length(canReceive) > 0L) pending <- pending[-canReceive] } if (verbose) { mdebugf("%s%d workers out of %d ready", verbose_prefix, ready, length(cl)) mdebugf_pop("%sWaiting for workers to connect back ... done", verbose_prefix) } } else if (setup_strategy == "sequential") { retryPort <- getOption2("parallelly.makeNodePSOCK.tries.port", "same") for (ii in seq_along(cl)) { if (verbose) { mdebugf_push("%sCreating node #%d of %d ...", verbose_prefix, ii, n) mdebugf("%ssetting up node", verbose_prefix) } options <- nodeOptions[[ii]] for (kk in 1:tries) { if (verbose) { mdebugf("%sattempt #%d of %d", verbose_prefix, kk, tries) } node <- tryCatch({ makeNode(options, verbose = verbose) }, error = identity) if (!inherits(node, "PSOCKConnectionError")) break if (kk < tries) { if (verbose) mdebug(conditionMessage(node)) if (retryPort == "next") { options$port <- min(options$port + 1L, 65535L) } else if (retryPort == "available") { options$port <- freePort() } if (verbose) { mdebugf("%swaiting %g seconds before trying again", verbose_prefix, delay) } Sys.sleep(delay) } } if (inherits(node, "error")) { ex <- node if (inherits(node, "PSOCKConnectionError")) { if (verbose) { mdebugf("%sFailed %d attempts with %g seconds delay", verbose_prefix, tries, delay) } ex$message <- sprintf("%s\n * Number of attempts: %d (%gs delay)", conditionMessage(ex), tries, delay) } else { ex$call <- sys.call() } stop(ex) } if (!is.null(node)) cl[[ii]] <- node stopifnot(length(cl) == n) if (verbose) { mdebugf_pop("%sCreating node #%d of %d ... done", verbose_prefix, ii, n) } } } if (verbose) { mdebugf("%sLaunching of %d workers completed", verbose_prefix, n) mdebugf("%sNumber of nodes in cluster: %d", verbose_prefix, length(cl)) } try(close(socket), silent = TRUE) socket <- NULL stopifnot(length(cl) == n) if (validate) { if (verbose) { mdebugf_push("%sCollecting session information from %d workers", verbose_prefix, length(cl)) } for (ii in seq_along(cl)) { cl[ii] <- add_cluster_session_info(cl[ii]) if (verbose) mdebugf("%sWorker #%d of %d", verbose_prefix, ii, length(cl)) } stopifnot(length(cl) == n) if (verbose) { mdebugf_pop("%sCollecting session information from %d workers", verbose_prefix, length(cl)) } } if (autoStop) { cl <- autoStopCluster(cl) stopifnot(length(cl) == n) if (verbose) mdebugf("%sAdded automatic stop of cluster on garbage collection", verbose_prefix) } stopifnot(length(cl) == n) on.exit() if (verbose) { mdebugf_pop("%smakeClusterPSOCK() ... done", verbose_prefix) options(oopts) } cl })(base::quote(2L), rscript_libs = base::quote(c("/tmp/Rtmp5gp92c/RLIBS_24912b38771cdf", "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/library")))`: Cluster setup failed (connectTimeout=125.0 seconds). 1 worker of 2 failed to connect.
Backtrace:
▆
1. ├─bamm::models2pam(...) at test-bam.R:473:3
2. │ └─future::plan(multisession, workers = ncores)
3. │ └─future (local) plan_set(...)
4. │ └─future:::plan_init(stack[[1]], debug = debug)
5. │ └─future:::makeFutureBackend(evaluator, debug = debug)
6. │ └─base::do.call(factory, args = args, envir = envir)
7. └─future (local) `<fn>`(workers = 2)
8. └─future::ClusterFutureBackend(...)
9. └─clusterRegistry$startCluster(...)
10. └─future (local) makeCluster(workers, ...)
11. ├─base::do.call(makeClusterPSOCK, args = args, quote = TRUE)
12. └─parallelly (local) `<fn>`(base::quote(2L), rscript_libs = base::quote(`<chr>`))
── Error ('test-bam.R:741:3'): predict retuns a prediction ─────────────────────
Error in `plot.new()`: could not open file '/tmp/RtmpkQf51T/Rplot1.png'
Backtrace:
▆
1. ├─stats::predict(...) at test-bam.R:741:3
2. └─bamm::predict(...)
3. └─bamm (local) .local(object, ...)
4. ├─animation::saveGIF(...)
5. │ └─animation:::in_dir(owd, expr)
6. ├─raster::plot(...)
7. └─raster::plot(...)
8. └─raster (local) .local(x, y, ...)
9. └─raster:::.plotraster2(...)
10. └─raster:::.rasterImagePlot(...)
11. ├─base::plot(...)
12. ├─base::plot(...)
13. └─graphics::plot.default(...)
14. └─graphics::plot.new()
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 62 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘bam.Rmd’ using rmarkdown
Warning in file("", "w+b") :
cannot open file '/tmp/RtmpFuGfpH/Rf2bad494dc6934': No space left on device
Quitting from bam.Rmd:102-104 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cannot open the connection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Quitting from bam.Rmd:102-104 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
file("", "w+b")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'bam.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘bam.Rmd’
SUMMARY: processing the following file failed:
‘bam.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc