##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:alabaster.sce.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings alabaster.sce_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.sce.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alabaster.sce/DESCRIPTION’ ... OK
* this is package ‘alabaster.sce’ version ‘1.7.0’
* 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 ‘alabaster.sce’ 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 whether startup messages can be suppressed ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  readSingleCellExperiment.Rd: SingleCellExperiment-class, readObject,
    saveObject, readObjectFile, readRangedSummarizedExperiment,
    altReadObject
  saveSingleCellExperiment.Rd: SingleCellExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* 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:
    3.   └─alabaster.sce (local) .local(x, dir, path, child, ...)
    4.     ├─methods::callNextMethod()
    5.     └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
    6.       └─alabaster.se (local) .local(x, dir, path, child, ...)
    7.         ├─methods::callNextMethod()
    8.         └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
    9.           └─alabaster.se (local) .local(x, dir, path, child, ...)
   10.             └─base::tryCatch(...)
   11.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   12.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13.                   └─value[[3L]](cond)
  
  [ FAIL 8 | WARN 0 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.sce.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.sce
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘alabaster.sce’ ...
** 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 (alabaster.sce)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(alabaster.sce)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians

Loading required package: alabaster.base

Attaching package: 'alabaster.base'

The following object is masked from 'package:Biobase':

    anyMissing

The following object is masked from 'package:matrixStats':

    anyMissing

> test_check("alabaster.sce")
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 3 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-SingleCellExperiment.R:18:5'): stageObject works as expected for SCE objects ──
Error in `value[[3L]](cond)`: failed to stage 'colData(<SingleCellExperiment>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
     ▆
  1. ├─alabaster.base::stageObject(se, tmp, "rnaseq") at test-SingleCellExperiment.R:18:5
  2. └─alabaster.sce::stageObject(se, tmp, "rnaseq")
  3.   └─alabaster.sce (local) .local(x, dir, path, child, ...)
  4.     ├─methods::callNextMethod()
  5.     └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
  6.       └─alabaster.se (local) .local(x, dir, path, child, ...)
  7.         ├─methods::callNextMethod()
  8.         └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
  9.           └─alabaster.se (local) .local(x, dir, path, child, ...)
 10.             └─base::tryCatch(...)
 11.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.                   └─value[[3L]](cond)
── Error ('test-SingleCellExperiment.R:60:5'): stageObject works as expected with reduced dims inside ──
Error in `value[[3L]](cond)`: failed to stage 'colData(<SingleCellExperiment>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
     ▆
  1. ├─alabaster.base::stageObject(se, tmp, "rnaseq") at test-SingleCellExperiment.R:60:5
  2. └─alabaster.sce::stageObject(se, tmp, "rnaseq")
  3.   └─alabaster.sce (local) .local(x, dir, path, child, ...)
  4.     ├─methods::callNextMethod()
  5.     └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
  6.       └─alabaster.se (local) .local(x, dir, path, child, ...)
  7.         ├─methods::callNextMethod()
  8.         └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
  9.           └─alabaster.se (local) .local(x, dir, path, child, ...)
 10.             └─base::tryCatch(...)
 11.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.                   └─value[[3L]](cond)
── Failure ('test-SingleCellExperiment.R:88:5'): stageObject fails with non-unique, non-empty reduced dim names ──
`info <- stageObject(se, tmp, "rnaseq")` threw an error with unexpected message.
Expected match: "duplicate"
Actual message: "failed to stage 'colData(<SingleCellExperiment>)'\n  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':\n  libnode.so.72: cannot open shared object file: No such file or directory"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-SingleCellExperiment.R:88:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─alabaster.base::stageObject(se, tmp, "rnaseq")
  7. └─alabaster.sce::stageObject(se, tmp, "rnaseq")
  8.   └─alabaster.sce (local) .local(x, dir, path, child, ...)
  9.     ├─methods::callNextMethod()
 10.     └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
 11.       └─alabaster.se (local) .local(x, dir, path, child, ...)
 12.         ├─methods::callNextMethod()
 13.         └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
 14.           └─alabaster.se (local) .local(x, dir, path, child, ...)
 15.             └─base::tryCatch(...)
 16.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 17.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 18.                   └─value[[3L]](cond)
── Failure ('test-SingleCellExperiment.R:92:5'): stageObject fails with non-unique, non-empty reduced dim names ──
`info <- stageObject(se, tmp, "rnaseq")` threw an error with unexpected message.
Expected match: "empty"
Actual message: "failed to stage 'colData(<SingleCellExperiment>)'\n  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':\n  libnode.so.72: cannot open shared object file: No such file or directory"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-SingleCellExperiment.R:92:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─alabaster.base::stageObject(se, tmp, "rnaseq")
  7. └─alabaster.sce::stageObject(se, tmp, "rnaseq")
  8.   └─alabaster.sce (local) .local(x, dir, path, child, ...)
  9.     ├─methods::callNextMethod()
 10.     └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
 11.       └─alabaster.se (local) .local(x, dir, path, child, ...)
 12.         ├─methods::callNextMethod()
 13.         └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
 14.           └─alabaster.se (local) .local(x, dir, path, child, ...)
 15.             └─base::tryCatch(...)
 16.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 17.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 18.                   └─value[[3L]](cond)
── Error ('test-SingleCellExperiment.R:102:5'): stageObject works as expected with alternative experiments inside ──
Error in `value[[3L]](cond)`: failed to stage 'colData(<SingleCellExperiment>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
     ▆
  1. ├─alabaster.base::stageObject(se, tmp, "rnaseq") at test-SingleCellExperiment.R:102:5
  2. └─alabaster.sce::stageObject(se, tmp, "rnaseq")
  3.   └─alabaster.sce (local) .local(x, dir, path, child, ...)
  4.     ├─methods::callNextMethod()
  5.     └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
  6.       └─alabaster.se (local) .local(x, dir, path, child, ...)
  7.         ├─methods::callNextMethod()
  8.         └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
  9.           └─alabaster.se (local) .local(x, dir, path, child, ...)
 10.             └─base::tryCatch(...)
 11.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.                   └─value[[3L]](cond)
── Failure ('test-SingleCellExperiment.R:128:5'): stageObject fails with non-unique, non-empty altexp names ──
`info <- stageObject(se, tmp, "rnaseq")` threw an error with unexpected message.
Expected match: "duplicate"
Actual message: "failed to stage 'colData(<SingleCellExperiment>)'\n  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':\n  libnode.so.72: cannot open shared object file: No such file or directory"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-SingleCellExperiment.R:128:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─alabaster.base::stageObject(se, tmp, "rnaseq")
  7. └─alabaster.sce::stageObject(se, tmp, "rnaseq")
  8.   └─alabaster.sce (local) .local(x, dir, path, child, ...)
  9.     ├─methods::callNextMethod()
 10.     └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
 11.       └─alabaster.se (local) .local(x, dir, path, child, ...)
 12.         ├─methods::callNextMethod()
 13.         └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
 14.           └─alabaster.se (local) .local(x, dir, path, child, ...)
 15.             └─base::tryCatch(...)
 16.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 17.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 18.                   └─value[[3L]](cond)
── Failure ('test-SingleCellExperiment.R:132:5'): stageObject fails with non-unique, non-empty altexp names ──
`info <- stageObject(se, tmp, "rnaseq")` threw an error with unexpected message.
Expected match: "empty"
Actual message: "failed to stage 'colData(<SingleCellExperiment>)'\n  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':\n  libnode.so.72: cannot open shared object file: No such file or directory"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-SingleCellExperiment.R:132:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─alabaster.base::stageObject(se, tmp, "rnaseq")
  7. └─alabaster.sce::stageObject(se, tmp, "rnaseq")
  8.   └─alabaster.sce (local) .local(x, dir, path, child, ...)
  9.     ├─methods::callNextMethod()
 10.     └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
 11.       └─alabaster.se (local) .local(x, dir, path, child, ...)
 12.         ├─methods::callNextMethod()
 13.         └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
 14.           └─alabaster.se (local) .local(x, dir, path, child, ...)
 15.             └─base::tryCatch(...)
 16.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 17.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 18.                   └─value[[3L]](cond)
── Error ('test-SingleCellExperiment.R:140:5'): stageObject works as expected when we slap in a main name ──
Error in `value[[3L]](cond)`: failed to stage 'colData(<SingleCellExperiment>)'
  - unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/V8/libs/V8.so':
  libnode.so.72: cannot open shared object file: No such file or directory
Backtrace:
     ▆
  1. ├─alabaster.base::stageObject(se, tmp, "rnaseq") at test-SingleCellExperiment.R:140:5
  2. └─alabaster.sce::stageObject(se, tmp, "rnaseq")
  3.   └─alabaster.sce (local) .local(x, dir, path, child, ...)
  4.     ├─methods::callNextMethod()
  5.     └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
  6.       └─alabaster.se (local) .local(x, dir, path, child, ...)
  7.         ├─methods::callNextMethod()
  8.         └─alabaster.se (local) .nextMethod(x = x, dir = dir, path = path)
  9.           └─alabaster.se (local) .local(x, dir, path, child, ...)
 10.             └─base::tryCatch(...)
 11.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.                   └─value[[3L]](cond)

[ FAIL 8 | WARN 0 | SKIP 0 | PASS 3 ]
Error: Test failures
Execution halted