##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:MultiAssayExperiment.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings MultiAssayExperiment_1.33.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MultiAssayExperiment.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 ‘MultiAssayExperiment/DESCRIPTION’ ... OK
* this is package ‘MultiAssayExperiment’ version ‘1.33.8’
* 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 ‘MultiAssayExperiment’ 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 ... WARNING
Missing or unexported object: ‘HDF5Array::h5writeDimnames’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MultiAssayExperiment-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HDF5MultiAssayExperiment
> ### Title: Save a MultiAssayExperiment class object to HDF5 and Rds files
> ### Aliases: HDF5MultiAssayExperiment saveHDF5MultiAssayExperiment
> ###   loadHDF5MultiAssayExperiment
> 
> ### ** Examples
> 
> 
> data("miniACC")
> 
> testDir <- file.path(tempdir(), "test_mae")
> 
> saveHDF5MultiAssayExperiment(
+     miniACC, dir = testDir, verbose = TRUE, replace = TRUE
+ )
Start writing assay 1/5 to HDF5 file:
  /tmp/RtmpIkh6qO/test_mae/miniACC_experiments.h5
/ reading and realizing block 1/1 ... ok
\ Writing it ... OK
Finished writing assay 1/5 to HDF5 file:
  /tmp/RtmpIkh6qO/test_mae/miniACC_experiments.h5

Start writing assay 2/5 to HDF5 file:
  /tmp/RtmpIkh6qO/test_mae/miniACC_experiments.h5
/ reading and realizing block 1/1 ... ok
\ Writing it ... OK
Finished writing assay 2/5 to HDF5 file:
  /tmp/RtmpIkh6qO/test_mae/miniACC_experiments.h5

Start writing assay 3/5 to HDF5 file:
  /tmp/RtmpIkh6qO/test_mae/miniACC_experiments.h5
/ reading and realizing block 1/1 ... ok
\ Writing it ... OK
Finished writing assay 3/5 to HDF5 file:
  /tmp/RtmpIkh6qO/test_mae/miniACC_experiments.h5

Start writing assay 4/5 to HDF5 file:
  /tmp/RtmpIkh6qO/test_mae/miniACC_experiments.h5
/ reading and realizing block 1/1 ... ok
\ Writing it ... OK
Finished writing assay 4/5 to HDF5 file:
  /tmp/RtmpIkh6qO/test_mae/miniACC_experiments.h5

Start writing assay 5/5 to HDF5 file:
  /tmp/RtmpIkh6qO/test_mae/miniACC_experiments.h5
/ reading and realizing block 1/1 ... ok
\ Writing it ... OK
Finished writing assay 5/5 to HDF5 file:
  /tmp/RtmpIkh6qO/test_mae/miniACC_experiments.h5

Error: 'h5writeDimnames' is not an exported object from 'namespace:HDF5Array'
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:
    1. └─MultiAssayExperiment::saveHDF5MultiAssayExperiment(...) at test-saveHDF5MultiAssayExperiment.R:113:5
    2.   └─MultiAssayExperiment:::.write_HDF5MultiAssayExperiment(...)
    3.     └─MultiAssayExperiment:::.write_h5_dimnames(assaylist, h5_path)
    4.       └─BiocGenerics::Map(...)
    5.         ├─BiocGenerics (local) standardGeneric("Map")
    6.         │ ├─BiocGenerics::eval(mc, env)
    7.         │ └─base::eval(mc, env)
    8.         │   └─base::eval(mc, env)
    9.         └─base::Map(f = f, ...)
   10.           └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
   11.             └─MultiAssayExperiment (local) `<fn>`(dl = dots[[1L]][[1L]], al = dots[[2L]][[1L]])
  
  [ FAIL 5 | WARN 40 | SKIP 1 | PASS 275 ]
  Error: Test failures
  Execution halted
* 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, 1 WARNING
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/MultiAssayExperiment.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL MultiAssayExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘MultiAssayExperiment’ ...
** this is package ‘MultiAssayExperiment’ version ‘1.33.8’
** using staged installation
** R
** data
** 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 (MultiAssayExperiment)

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(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

> 
> example("MultiAssayExperiment")

MltAsE> ## Run the example ExperimentList
MltAsE> example("ExperimentList")

ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
ExperimentList class object of length 0:
 
ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000294241", "ENST00000355076",
ExprmL+         "ENST00000383706","ENST00000234812", "ENST00000383323"),
ExprmL+         c("array1", "array2", "array3", "array4")
ExprmL+     ))

ExprmL> colDat <- data.frame(slope53 = rnorm(4),
ExprmL+     row.names = c("array1", "array2", "array3", "array4"))

ExprmL> ## SummarizedExperiment constructor
ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat,
ExprmL+     colData = colDat)

ExprmL> ## Create a sample methylation dataset
ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000355076", "ENST00000383706",
ExprmL+           "ENST00000383323", "ENST00000234812", "ENST00000294241"),
ExprmL+         c("methyl1", "methyl2", "methyl3",
ExprmL+           "methyl4", "methyl5")
ExprmL+     ))

ExprmL> ## Create a sample RNASeqGene dataset
ExprmL> rnadat <- matrix(
ExprmL+     data = sample(c(46851, 5, 19, 13, 2197, 507,
ExprmL+         84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
ExprmL+     ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
ExprmL+         c("samparray1", "samparray2", "samparray3", "samparray4")
ExprmL+     ))

ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame
ExprmL> rangedat <- data.frame(chr="chr2", start = 11:15, end = 12:16,
ExprmL+     strand = c("+", "-", "+", "*", "."),
ExprmL+     samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0),
ExprmL+     row.names = c(paste0("ENST", "00000", 135411:135414), "ENST00000383323"))

ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat)

ExprmL> ## Combine to a named list and call the ExperimentList constructor function
ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat,
ExprmL+                 GISTIC = rangeSE)

ExprmL> ## Use the ExperimentList constructor
ExprmL> ExpList <- ExperimentList(assayList)

MltAsE> ## Create sample maps for each experiment
MltAsE> exprmap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("array1", "array2", "array3", "array4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> methylmap <- data.frame(
MltAsE+     primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> rnamap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Bob", "Barbara"),
MltAsE+     colname = c("samparray1", "samparray2", "samparray3", "samparray4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> gistmap <- data.frame(
MltAsE+     primary = c("Jack", "Bob", "Jill"),
MltAsE+     colname = c("samp0", "samp1", "samp2"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> ## Combine as a named list and convert to a DataFrame
MltAsE> maplist <- list(Affy = exprmap, Methyl450k = methylmap,
MltAsE+     RNASeqGene = rnamap, GISTIC = gistmap)

MltAsE> ## Create a sampleMap
MltAsE> sampMap <- listToMap(maplist)

MltAsE> ## Create an example phenotype data
MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"), age = 38:41,
MltAsE+     row.names = c("Jack", "Jill", "Bob", "Barbara"))

MltAsE> ## Create a MultiAssayExperiment instance
MltAsE> mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat,
MltAsE+     sampleMap = sampMap)
> 
> test_check("MultiAssayExperiment")
[ FAIL 5 | WARN 40 | SKIP 1 | PASS 275 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-listToMap.R:3:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-saveHDF5MultiAssayExperiment.R:9:5'): saveHDF5MultiAssayExperiment is working ──
Error: 'h5writeDimnames' is not an exported object from 'namespace:HDF5Array'
Backtrace:
     ▆
  1. └─MultiAssayExperiment::saveHDF5MultiAssayExperiment(...) at test-saveHDF5MultiAssayExperiment.R:9:5
  2.   └─MultiAssayExperiment:::.write_HDF5MultiAssayExperiment(...)
  3.     └─MultiAssayExperiment:::.write_h5_dimnames(assaylist, h5_path)
  4.       └─BiocGenerics::Map(...)
  5.         ├─BiocGenerics (local) standardGeneric("Map")
  6.         │ ├─BiocGenerics::eval(mc, env)
  7.         │ └─base::eval(mc, env)
  8.         │   └─base::eval(mc, env)
  9.         └─base::Map(f = f, ...)
 10.           └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 11.             └─MultiAssayExperiment (local) `<fn>`(dl = dots[[1L]][[1L]], al = dots[[2L]][[1L]])
── Error ('test-saveHDF5MultiAssayExperiment.R:37:5'): prefix argument works as intended ──
Error: 'h5writeDimnames' is not an exported object from 'namespace:HDF5Array'
Backtrace:
     ▆
  1. └─MultiAssayExperiment::saveHDF5MultiAssayExperiment(...) at test-saveHDF5MultiAssayExperiment.R:37:5
  2.   └─MultiAssayExperiment:::.write_HDF5MultiAssayExperiment(...)
  3.     └─MultiAssayExperiment:::.write_h5_dimnames(assaylist, h5_path)
  4.       └─BiocGenerics::Map(...)
  5.         ├─BiocGenerics (local) standardGeneric("Map")
  6.         │ ├─BiocGenerics::eval(mc, env)
  7.         │ └─base::eval(mc, env)
  8.         │   └─base::eval(mc, env)
  9.         └─base::Map(f = f, ...)
 10.           └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 11.             └─MultiAssayExperiment (local) `<fn>`(dl = dots[[1L]][[1L]], al = dots[[2L]][[1L]])
── Error ('test-saveHDF5MultiAssayExperiment.R:71:5'): array assays work with saveHDF5MultiAssayExperiment ──
Error: 'h5writeDimnames' is not an exported object from 'namespace:HDF5Array'
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test-saveHDF5MultiAssayExperiment.R:71:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─MultiAssayExperiment::saveHDF5MultiAssayExperiment(...)
  7.   └─MultiAssayExperiment:::.write_HDF5MultiAssayExperiment(...)
  8.     └─MultiAssayExperiment:::.write_h5_dimnames(assaylist, h5_path)
  9.       └─BiocGenerics::Map(...)
 10.         ├─BiocGenerics (local) standardGeneric("Map")
 11.         │ ├─BiocGenerics::eval(mc, env)
 12.         │ └─base::eval(mc, env)
 13.         │   └─base::eval(mc, env)
 14.         └─base::Map(f = f, ...)
 15.           └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 16.             └─MultiAssayExperiment (local) `<fn>`(dl = dots[[1L]][[1L]], al = dots[[2L]][[1L]])
── Error ('test-saveHDF5MultiAssayExperiment.R:93:5'): loadHDF5MultiAssayExperiment is working ──
Error: 'h5writeDimnames' is not an exported object from 'namespace:HDF5Array'
Backtrace:
     ▆
  1. └─MultiAssayExperiment::saveHDF5MultiAssayExperiment(...) at test-saveHDF5MultiAssayExperiment.R:93:5
  2.   └─MultiAssayExperiment:::.write_HDF5MultiAssayExperiment(...)
  3.     └─MultiAssayExperiment:::.write_h5_dimnames(assaylist, h5_path)
  4.       └─BiocGenerics::Map(...)
  5.         ├─BiocGenerics (local) standardGeneric("Map")
  6.         │ ├─BiocGenerics::eval(mc, env)
  7.         │ └─base::eval(mc, env)
  8.         │   └─base::eval(mc, env)
  9.         └─base::Map(f = f, ...)
 10.           └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 11.             └─MultiAssayExperiment (local) `<fn>`(dl = dots[[1L]][[1L]], al = dots[[2L]][[1L]])
── Error ('test-saveHDF5MultiAssayExperiment.R:113:5'): loadHDF5MultiAssayExperiment prefix input is consistent ──
Error: 'h5writeDimnames' is not an exported object from 'namespace:HDF5Array'
Backtrace:
     ▆
  1. └─MultiAssayExperiment::saveHDF5MultiAssayExperiment(...) at test-saveHDF5MultiAssayExperiment.R:113:5
  2.   └─MultiAssayExperiment:::.write_HDF5MultiAssayExperiment(...)
  3.     └─MultiAssayExperiment:::.write_h5_dimnames(assaylist, h5_path)
  4.       └─BiocGenerics::Map(...)
  5.         ├─BiocGenerics (local) standardGeneric("Map")
  6.         │ ├─BiocGenerics::eval(mc, env)
  7.         │ └─base::eval(mc, env)
  8.         │   └─base::eval(mc, env)
  9.         └─base::Map(f = f, ...)
 10.           └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 11.             └─MultiAssayExperiment (local) `<fn>`(dl = dots[[1L]][[1L]], al = dots[[2L]][[1L]])

[ FAIL 5 | WARN 40 | SKIP 1 | PASS 275 ]
Error: Test failures
Execution halted