##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:alabaster.mae.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings alabaster.mae_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.mae.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.mae/DESCRIPTION’ ... OK
* this is package ‘alabaster.mae’ 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.mae’ 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:
  readMultiAssayExperiment.Rd: MultiAssayExperiment-class, readObject,
    stageObject, readObjectFile, altReadObject
  saveMultiAssayExperiment.Rd: MultiAssayExperiment-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 ... ERROR
Running examples in ‘alabaster.mae-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readMultiAssayExperiment
> ### Title: Read a MultiAssayExperiment from disk
> ### Aliases: readMultiAssayExperiment loadMultiAssayExperiment
> 
> ### ** Examples
> 
> library(SummarizedExperiment)
> 
> # Mocking up an MAE
> mat <- matrix(rnorm(1000), ncol=10)
> colnames(mat) <- letters[1:10]
> rownames(mat) <- sprintf("GENE_%i", seq_len(nrow(mat)))
> se <- SummarizedExperiment(list(counts=mat))
> 
> library(MultiAssayExperiment)
> mae <- MultiAssayExperiment(list(gene=se))
> 
> # Staging it:
> tmp <- tempfile()
> dir.create(tmp)
> info <- stageObject(mae, tmp, "dataset")
Error in value[[3L]](cond) : 
  failed to stage 'sampleMap(<MultiAssayExperiment>)'
  - 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
Calls: stageObject ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* 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:
    - 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(mae, temp, "whee") at test-stage-mae.R:142:5
   2. └─alabaster.mae::stageObject(mae, temp, "whee")
   3.   └─alabaster.mae (local) .local(x, dir, path, child, ...)
   4.     └─base::tryCatch(...)
   5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.           └─value[[3L]](cond)
  
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 11 ]
  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: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.mae.Rcheck/00check.log’
for details.

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


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

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.mae)
Loading required package: MultiAssayExperiment
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.mae")
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 11 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-stage-mae.R:20:5'): stageMultiAssayExperiment works as expected ──
Error in `value[[3L]](cond)`: failed to stage 'sampleMap(<MultiAssayExperiment>)'
  - 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(mae, temp, path = "thing") at test-stage-mae.R:20:5
 2. └─alabaster.mae::stageObject(mae, temp, path = "thing")
 3.   └─alabaster.mae (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
── Error ('test-stage-mae.R:47:5'): stageMultiAssayExperiment works as expected with non-empty colData ──
Error in `value[[3L]](cond)`: failed to stage 'sampleMap(<MultiAssayExperiment>)'
  - 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(mae, temp, path = "thing") at test-stage-mae.R:47:5
 2. └─alabaster.mae::stageObject(mae, temp, path = "thing")
 3.   └─alabaster.mae (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
── Error ('test-stage-mae.R:61:5'): stageMultiAssayExperiment works as expected with non-trivial sample mappings ──
Error in `value[[3L]](cond)`: failed to stage 'sampleMap(<MultiAssayExperiment>)'
  - 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(mae, temp, "whee") at test-stage-mae.R:61:5
 2. └─alabaster.mae::stageObject(mae, temp, "whee")
 3.   └─alabaster.mae (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
── Error ('test-stage-mae.R:88:5'): stageMultiAssayExperiment respects entries in the metadata ──
Error in `value[[3L]](cond)`: failed to stage 'sampleMap(<MultiAssayExperiment>)'
  - 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(mae, temp, path = "thing") at test-stage-mae.R:88:5
 2. └─alabaster.mae::stageObject(mae, temp, path = "thing")
 3.   └─alabaster.mae (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
── Error ('test-stage-mae.R:104:5'): loadMultiAssayExperiment works as expected with restricted experiments ──
Error in `value[[3L]](cond)`: failed to stage 'sampleMap(<MultiAssayExperiment>)'
  - 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(mae, temp, "whee") at test-stage-mae.R:104:5
 2. └─alabaster.mae::stageObject(mae, temp, "whee")
 3.   └─alabaster.mae (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
── Error ('test-stage-mae.R:129:5'): loadMultiAssayExperiment works as expected with parallelization ──
Error in `value[[3L]](cond)`: failed to stage 'sampleMap(<MultiAssayExperiment>)'
  - 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(mae, temp, "whee") at test-stage-mae.R:129:5
 2. └─alabaster.mae::stageObject(mae, temp, "whee")
 3.   └─alabaster.mae (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
── Error ('test-stage-mae.R:142:5'): loadMultiAssayExperiment allows us to request no-nesting ──
Error in `value[[3L]](cond)`: failed to stage 'sampleMap(<MultiAssayExperiment>)'
  - 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(mae, temp, "whee") at test-stage-mae.R:142:5
 2. └─alabaster.mae::stageObject(mae, temp, "whee")
 3.   └─alabaster.mae (local) .local(x, dir, path, child, ...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)

[ FAIL 7 | WARN 0 | SKIP 0 | PASS 11 ]
Error: Test failures
Execution halted