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### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:tximport.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings tximport_1.35.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/tximport.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘tximport/DESCRIPTION’ ... OK
* this is package ‘tximport’ version ‘1.35.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tximport’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘tximport-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tximport
> ### Title: Import transcript-level abundances and counts for transcript-
> ###   and gene-level analysis packages
> ### Aliases: tximport
> 
> ### ** Examples
> 
> 
> # load data for demonstrating tximport
> # note that the vignette shows more examples
> # including how to read in files quickly using the readr package
> 
> library(tximportData)
> dir <- system.file("extdata", package="tximportData")
> samples <- read.table(file.path(dir,"samples.txt"), header=TRUE)
> files <- file.path(dir,"salmon", samples$run, "quant.sf.gz")
> names(files) <- paste0("sample",1:6)
> 
> # tx2gene links transcript IDs to gene IDs for summarization
> tx2gene <- read.csv(file.path(dir, "tx2gene.gencode.v27.csv"))
> 
> txi <- tximport(files, type="salmon", tx2gene=tx2gene)
reading in files with read_tsv
1 
 *** caught segfault ***
address 0x734934ec6000, cause 'memory not mapped'

Traceback:
 1: vroom_(file, delim = delim %||% col_types$delim, col_names = col_names,     col_types = col_types, id = id, skip = skip, col_select = col_select,     name_repair = .name_repair, na = na, quote = quote, trim_ws = trim_ws,     escape_double = escape_double, escape_backslash = escape_backslash,     comment = comment, skip_empty_rows = skip_empty_rows, locale = locale,     guess_max = guess_max, n_max = n_max, altrep = vroom_altrep(altrep),     num_threads = num_threads, progress = progress)
 2: vroom::vroom(file, delim = "\t", col_names = col_names, col_types = col_types,     col_select = {        {            col_select        }    }, id = id, .name_repair = name_repair, skip = skip, n_max = n_max,     na = na, quote = quote, comment = comment, skip_empty_rows = skip_empty_rows,     trim_ws = trim_ws, escape_double = TRUE, escape_backslash = FALSE,     locale = locale, guess_max = guess_max, show_col_types = show_col_types,     progress = progress, altrep = lazy, num_threads = num_threads)
 3: readr::read_tsv(x, progress = FALSE, col_types = col.types)
 4: importer(files[i])
 5: as.data.frame(importer(files[i]))
 6: tximport(files, type = "salmon", tx2gene = tx2gene)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  29: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  30: source_file(path, env = env(env), desc = desc, error_call = error_call)
  31: FUN(X[[i]], ...)
  32: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  33: doTryCatch(return(expr), name, parentenv, handler)
  34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  35: tryCatchList(expr, classes, parentenv, handlers)
  36: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  37: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  38: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
  39: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
  40: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  41: test_check("tximport")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault (core dumped)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/tximport.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL tximport
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘tximport’ ...
** this is package ‘tximport’ version ‘1.35.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tximport)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(tximport)
> library(tximportData)
> library(readr)

Attaching package: 'readr'

The following objects are masked from 'package:testthat':

    edition_get, local_edition

> test_check("tximport")

 *** caught segfault ***
address 0x78dcfb680000, cause 'memory not mapped'

Traceback:
 1: vroom_(file, delim = delim %||% col_types$delim, col_names = col_names,     col_types = col_types, id = id, skip = skip, col_select = col_select,     name_repair = .name_repair, na = na, quote = quote, trim_ws = trim_ws,     escape_double = escape_double, escape_backslash = escape_backslash,     comment = comment, skip_empty_rows = skip_empty_rows, locale = locale,     guess_max = guess_max, n_max = n_max, altrep = vroom_altrep(altrep),     num_threads = num_threads, progress = progress)
 2: vroom::vroom(file, delim = "\t", col_names = col_names, col_types = col_types,     col_select = {        {            col_select        }    }, id = id, .name_repair = name_repair, skip = skip, n_max = n_max,     na = na, quote = quote, comment = comment, skip_empty_rows = skip_empty_rows,     trim_ws = trim_ws, escape_double = TRUE, escape_backslash = FALSE,     locale = locale, guess_max = guess_max, show_col_types = show_col_types,     progress = progress, altrep = lazy, num_threads = num_threads)
 3: readr::read_tsv(x, progress = FALSE, col_types = col.types)
 4: importer(files[i])
 5: as.data.frame(importer(files[i]))
 6: tximport(files, type = "salmon", tx2gene = tx2gene)
 7: eval(code, test_env)
 8: eval(code, test_env)
 9: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
15: tryCatchList(expr, classes, parentenv, handlers)
16: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
17: test_code(desc, code, env = parent.frame(), reporter = reporter)
18: test_that("getting counts from abundance works", {    library(readr)    dir <- system.file("extdata", package = "tximportData")    samples <- read.table(file.path(dir, "samples.txt"), header = TRUE)    files <- file.path(dir, "salmon", samples$run, "quant.sf.gz")    names(files) <- paste0("sample", 1:6)    tx2gene <- read_csv(file.path(dir, "tx2gene.gencode.v27.csv"))    txi <- tximport(files, type = "salmon", tx2gene = tx2gene)    txi.S <- tximport(files, type = "salmon", tx2gene = tx2gene,         countsFromAbundance = "scaledTPM")    txi.LS <- tximport(files, type = "salmon", tx2gene = tx2gene,         countsFromAbundance = "lengthScaledTPM")    expect_true(ncol(txi.S$counts) == length(files))    expect_true(ncol(txi.LS$counts) == length(files))    txi.tx <- tximport(files, type = "salmon", txOut = TRUE,         countsFromAbundance = "no")    txi.tx.S <- tximport(files, type = "salmon", txOut = TRUE,         countsFromAbundance = "scaledTPM")    txi.tx.LS <- tximport(files, type = "salmon", txOut = TRUE,         countsFromAbundance = "lengthScaledTPM")    expect_true(!all(txi$counts[, 1] == txi.S$counts[, 1]))    expect_true(!all(txi$counts[, 1] == txi.LS$counts[, 1]))    expect_warning({        txi.sum.S <- summarizeToGene(txi.tx.S, tx2gene = tx2gene,             countsFromAbundance = "no")    }, "incoming counts")    expect_true(txi.sum.S$countsFromAbundance == "scaledTPM")    expect_warning({        txi.sum.LS <- summarizeToGene(txi.tx.LS, tx2gene = tx2gene,             countsFromAbundance = "no")    }, "incoming counts")    expect_true(txi.sum.LS$countsFromAbundance == "lengthScaledTPM")    txi.tx.dtu <- tximport(files, type = "salmon", tx2gene = tx2gene,         txOut = TRUE, countsFromAbundance = "dtuScaledTPM")    expect_error(tximport(files, type = "salmon", txOut = TRUE,         countsFromAbundance = "dtuScaledTPM"))    expect_error(tximport(files, type = "salmon", tx2gene = tx2gene,         txOut = FALSE, countsFromAbundance = "dtuScaledTPM"))})
19: eval(code, test_env)
20: eval(code, test_env)
21: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
29: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
30: source_file(path, env = env(env), desc = desc, error_call = error_call)
31: FUN(X[[i]], ...)
32: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
37: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
38: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
39: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
40: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
41: test_check("tximport")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)