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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SummarizedExperiment.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SummarizedExperiment_1.41.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SummarizedExperiment.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SummarizedExperiment/DESCRIPTION’ ... OK
* this is package ‘SummarizedExperiment’ version ‘1.41.1’
* 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 ‘SummarizedExperiment’ 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    BUG FIXES
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RangedSummarizedExperiment-class.Rd: GRanges, GRangesList, DataFrame,
    pcompare, end<-, granges, mcols, mcols<-, ranges, ranges<-,
    seqinfo, seqinfo<-, seqnames, start<-, strand, strand<-, width,
    width<-
  SummarizedExperiment-class.Rd: DataFrame, SimpleList, DelayedArray
  makeSummarizedExperimentFromDataFrame.Rd: GRanges,
    makeGRangesFromDataFrame, Seqinfo
  makeSummarizedExperimentFromExpressionSet.Rd: GRanges, GRangesList
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 ‘SummarizedExperiment-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeSummarizedExperimentFromExpressionSet
> ### Title: Make a RangedSummarizedExperiment object from an ExpressionSet
> ###   and vice-versa
> ### Aliases: makeSummarizedExperimentFromExpressionSet naiveRangeMapper
> ###   probeRangeMapper geneRangeMapper
> ###   coerce,ExpressionSet,RangedSummarizedExperiment-method
> ###   coerce,ExpressionSet,SummarizedExperiment-method
> ###   coerce,RangedSummarizedExperiment,ExpressionSet-method
> ###   coerce,SummarizedExperiment,ExpressionSet-method
> ### Keywords: manip
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## GOING FROM ExpressionSet TO SummarizedExperiment
> ## ---------------------------------------------------------------------
> 
> data(sample.ExpressionSet, package="Biobase")
> 
> # naive coercion
> makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet)
class: RangedSummarizedExperiment 
dim: 500 26 
metadata(3): experimentData annotation protocolData
assays(2): exprs se.exprs
rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
rowData names(0):
colnames(26): A B ... Y Z
colData names(3): sex type score
> as(sample.ExpressionSet, "RangedSummarizedExperiment")
class: RangedSummarizedExperiment 
dim: 500 26 
metadata(3): experimentData annotation protocolData
assays(2): exprs se.exprs
rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
rowData names(0):
colnames(26): A B ... Y Z
colData names(3): sex type score
> as(sample.ExpressionSet, "SummarizedExperiment")
class: SummarizedExperiment 
dim: 500 26 
metadata(3): experimentData annotation protocolData
assays(2): exprs se.exprs
rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
rowData names(0):
colnames(26): A B ... Y Z
colData names(3): sex type score
> 
> # using probe range mapper
> makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet, probeRangeMapper)


Warning in .deprecatedColsMessage() :
  Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
  deprecated. Please use a range based accessor like genes(), or select() with
  columns values like TXCHROM and TXSTART on a TxDb or OrganismDb object
  instead.
'select()' returned 1:many mapping between keys and columns
Warning: 148 probes could not be mapped.
class: RangedSummarizedExperiment 
dim: 352 26 
metadata(3): experimentData annotation protocolData
assays(2): exprs se.exprs
rownames(352): AFFX-HUMISGF3A/M97935_5_at AFFX-HUMISGF3A/M97935_MA_at
  ... 31736_at 31737_at
rowData names(0):
colnames(26): A B ... Y Z
colData names(3): sex type score
> 
> # using the gene range mapper
> se <- makeSummarizedExperimentFromExpressionSet(
+     sample.ExpressionSet,
+     geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene")
+ )
'select()' returned 1:many mapping between keys and columns
Error: Failed to load ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ package
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
   
  1 Test Suite : 
  SummarizedExperiment RUnit Tests - 46 test functions, 1 error, 0 failures
  ERROR in test_GenomicRanges_SummarizedExperiment_coercion_mappingFunctions: Error : Failed to load 'TxDb.Hsapiens.UCSC.hg19.knownGene' package
  
  Test files with failing tests
  
     test_makeSummarizedExperimentFromExpressionSet.R 
       test_GenomicRanges_SummarizedExperiment_coercion_mappingFunctions 
  
  
  Error in BiocGenerics:::testPackage("SummarizedExperiment") : 
    unit tests failed for package SummarizedExperiment
  Calls: <Anonymous> -> <Anonymous>
  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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/SummarizedExperiment.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SummarizedExperiment
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘SummarizedExperiment’ ...
** this is package ‘SummarizedExperiment’ version ‘1.41.1’
** 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 (SummarizedExperiment)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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.

> require("SummarizedExperiment") || stop("unable to load SummarizedExperiment package")
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: Seqinfo
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

[1] TRUE
> SummarizedExperiment:::.test()


'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Timing stopped at: 5.225 0.998 6.236
Error : Failed to load 'TxDb.Hsapiens.UCSC.hg19.knownGene' package
In addition: Warning messages:
1: In normarg_mcols(value, class(x), length(x)) :
  You supplied a metadata column of length 2 to set on an object of length 5.
  However please note that the latter is not a multiple of the former.
2: In normarg_mcols(value, class(x), length(x)) :
  You supplied metadata columns of length 2 to set on an object of length 3.
  However please note that the latter is not a multiple of the former.
3: In S4Vectors:::V_recycle(arg, x, argname, "x") :
  'length(x)' is not a multiple of 'NROW(weight)'
4: In S4Vectors:::V_recycle(arg, x, argname, "x") :
  'length(x)' is not a multiple of 'NROW(weight)'
5: In .deprecatedColsMessage() :
  Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
  deprecated. Please use a range based accessor like genes(), or select() with
  columns values like TXCHROM and TXSTART on a TxDb or OrganismDb object
  instead.
6: 148 probes could not be mapped. 


RUNIT TEST PROTOCOL -- Fri Apr 17 06:31:21 2026 
*********************************************** 
Number of test functions: 46 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
SummarizedExperiment RUnit Tests - 46 test functions, 1 error, 0 failures
ERROR in test_GenomicRanges_SummarizedExperiment_coercion_mappingFunctions: Error : Failed to load 'TxDb.Hsapiens.UCSC.hg19.knownGene' package

Test files with failing tests

   test_makeSummarizedExperimentFromExpressionSet.R 
     test_GenomicRanges_SummarizedExperiment_coercion_mappingFunctions 


Error in BiocGenerics:::testPackage("SummarizedExperiment") : 
  unit tests failed for package SummarizedExperiment
Calls: <Anonymous> -> <Anonymous>
Execution halted