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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SingleCellAlleleExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SingleCellAlleleExperiment_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SingleCellAlleleExperiment.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SingleCellAlleleExperiment/DESCRIPTION’ ... OK
* this is package ‘SingleCellAlleleExperiment’ version ‘1.0.0’
* 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 ‘SingleCellAlleleExperiment’ 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 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 ‘SingleCellAlleleExperiment-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SingleCellAlleleExperiment-class
> ### Title: The SingleCellAlleleExperiment class
> ### Aliases: SingleCellAlleleExperiment-class .scae
> ###   SingleCellAlleleExperiment
> 
> ### ** Examples
> 
> ##-If you want to use the Constructor on its own, some preprocessing is
> ##-necessary to bring the data in proper format
> ##-Here, we use an example dataset found in in the `scaeData` package.
> 
> ##-Find an alternative and recommended read in below as a second example
> 
> example_data_5k <- scaeData::scaeDataGet(dataset="pbmc_5k")
Retrieving barcode identifiers for **pbmc 5k** dataset...DONE
Retrieving feature identifiers for **pbmc 5k** dataset...DONE
Retrieving quantification matrix for **pbmc 5k** dataset...DONE
> lookup_name <- "pbmc_5k_lookup_table.csv"
> lookup <- read.csv(system.file("extdata", lookup_name, package="scaeData"))
> 
> barcode_loc <- file.path(example_data_5k$dir, example_data_5k$barcodes)
> feature_loc <- file.path(example_data_5k$dir, example_data_5k$features)
> matrix_loc  <- file.path(example_data_5k$dir, example_data_5k$matrix)
> 
> feature_info <- utils::read.delim(feature_loc, header=FALSE)
> cell_names   <- utils::read.csv(barcode_loc, sep="", header=FALSE)
> mat <- t(Matrix::readMM(matrix_loc))
> 
> ##-Prepare input data
> colnames(feature_info) <- "Ensembl_ID"
> sample_names <- "pbmc_5k"
> sparse_mat <- as(mat, "CsparseMatrix")
> 
> ##--colData
> cell_info_list <- S4Vectors::DataFrame(Sample=rep(sample_names,
+                                                  length(cell_names)),
+                                       Barcode=cell_names$V1,
+                                       row.names=NULL)
> ##--rowData and count matrix
> rownames(feature_info) <- feature_info[,1]
> cnames <- cell_info_list$Barcode
> colnames(sparse_mat) <- cnames
> 
> scae <- SingleCellAlleleExperiment(assays=list(counts=sparse_mat),
+                                    rowData=feature_info,
+                                    colData=cell_info_list,
+                                    lookup=lookup,
+                                    verbose=TRUE)
  Generating SCAE object: Extending rowData with new classifiers
  Generating SCAE object: Filtering at 0 UMI counts.
  Generating SCAE object: Compute Library Factors before adding new layers
Error in fixupDN.if.valid(value, x@Dim) : 
  length of Dimnames[[1]] (6) is not equal to Dim[1] (12)
Calls: SingleCellAlleleExperiment ... rownames<- -> dimnames<- -> dimnames<- -> fixupDN.if.valid
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:
  Error in `fixupDN.if.valid(value, x@Dim)`: length of Dimnames[[1]] (6) is not equal to Dim[1] (12)
  Backtrace:
      ▆
   1. └─SingleCellAlleleExperiment::read_allele_counts(...) at test-scaeSubset.R:10:1
   2.   └─SingleCellAlleleExperiment::SingleCellAlleleExperiment(...)
   3.     └─SingleCellAlleleExperiment:::alleles2genes(...)
   4.       └─SingleCellAlleleExperiment:::get_allelecounts(sce, lookup)
   5.         └─base::`rownames<-`(`*tmp*`, value = alid_gene_names)
   6.           ├─methods (local) `dimnames<-`(`*tmp*`, value = dn)
   7.           └─Matrix (local) `dimnames<-`(`*tmp*`, value = dn)
   8.             └─Matrix:::fixupDN.if.valid(value, x@Dim)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  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
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/SingleCellAlleleExperiment.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleCellAlleleExperiment
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘SingleCellAlleleExperiment’ ...
** using staged installation
** R
** 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 (SingleCellAlleleExperiment)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> # 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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(SingleCellAlleleExperiment)
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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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

> library(scaeData)
> 
> test_check("SingleCellAlleleExperiment")

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Retrieving barcode identifiers for **pbmc 5k** dataset...DONE
Retrieving feature identifiers for **pbmc 5k** dataset...DONE
Retrieving quantification matrix for **pbmc 5k** dataset...DONE

Data Read_in completed
Using org.Hs to retrieve NCBI gene identifiers.
  Generating SCAE object: Extending rowData with new classifiers
  Generating SCAE object: Filtering at 0 UMI counts.
Retrieving barcode identifiers for **pbmc 5k** dataset...DONE
Retrieving feature identifiers for **pbmc 5k** dataset...DONE
Retrieving quantification matrix for **pbmc 5k** dataset...DONE
Filtering performed based on the inflection point at: 911 UMI counts.
Data Read_in completed
  Generating SCAE object: Extending rowData with new classifiers
  Generating SCAE object: Filtering at 911 UMI counts.
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-SingleCellAlleleExperiment.R:33:1'): (code run outside of `test_that()`) ──
Error in `fixupDN.if.valid(value, x@Dim)`: length of Dimnames[[1]] (6) is not equal to Dim[1] (12)
Backtrace:
    ▆
 1. └─SingleCellAlleleExperiment::read_allele_counts(...) at test-SingleCellAlleleExperiment.R:33:1
 2.   └─SingleCellAlleleExperiment::SingleCellAlleleExperiment(...)
 3.     └─SingleCellAlleleExperiment:::alleles2genes(...)
 4.       └─SingleCellAlleleExperiment:::get_allelecounts(sce, lookup)
 5.         └─base::`rownames<-`(`*tmp*`, value = alid_gene_names)
 6.           ├─methods (local) `dimnames<-`(`*tmp*`, value = dn)
 7.           └─Matrix (local) `dimnames<-`(`*tmp*`, value = dn)
 8.             └─Matrix:::fixupDN.if.valid(value, x@Dim)
── Error ('test-scaeSubset.R:10:1'): (code run outside of `test_that()`) ───────
Error in `fixupDN.if.valid(value, x@Dim)`: length of Dimnames[[1]] (6) is not equal to Dim[1] (12)
Backtrace:
    ▆
 1. └─SingleCellAlleleExperiment::read_allele_counts(...) at test-scaeSubset.R:10:1
 2.   └─SingleCellAlleleExperiment::SingleCellAlleleExperiment(...)
 3.     └─SingleCellAlleleExperiment:::alleles2genes(...)
 4.       └─SingleCellAlleleExperiment:::get_allelecounts(sce, lookup)
 5.         └─base::`rownames<-`(`*tmp*`, value = alid_gene_names)
 6.           ├─methods (local) `dimnames<-`(`*tmp*`, value = dn)
 7.           └─Matrix (local) `dimnames<-`(`*tmp*`, value = dn)
 8.             └─Matrix:::fixupDN.if.valid(value, x@Dim)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted