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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GenomicFeatures_1.54.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicFeatures.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.54.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GenomicFeatures’ 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 R 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 ... NOTE
':::' call which should be '::': ‘rtracklayer:::tableNames’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.valid.colnames’
  ‘AnnotationDbi:::.valid.metadata.table’
  ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’
  ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’
  ‘BiocGenerics:::testPackage’ ‘GenomeInfoDb:::check_tax_id’
  ‘GenomeInfoDb:::getSeqlevelsReplacementMode’
  ‘GenomeInfoDb:::lookup_organism_by_tax_id’
  ‘GenomeInfoDb:::lookup_tax_id_by_organism’
  ‘GenomeInfoDb:::make_circ_flags_from_circ_seqs’
  ‘GenomeInfoDb:::normarg_new2old’
  ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’
  ‘GenomicRanges:::unsafe.transcriptWidths’
  ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::V_recycle’
  ‘S4Vectors:::anyMissingOrOutside’ ‘S4Vectors:::decodeRle’
  ‘S4Vectors:::extract_data_frame_rows’ ‘S4Vectors:::quick_togroup’
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::resourceDescription’
  See the note in ?`:::` about the use of this operator.
* 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 ‘GenomicFeatures-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mapToTranscripts
> ### Title: Map range coordinates between transcripts and genome space
> ### Aliases: coordinate-mapping mapToTranscripts
> ###   mapToTranscripts,GenomicRanges,GenomicRanges-method
> ###   mapToTranscripts,GenomicRanges,GRangesList-method
> ###   mapToTranscripts,ANY,TxDb-method pmapToTranscripts
> ###   pmapToTranscripts,GenomicRanges,GenomicRanges-method
> ###   pmapToTranscripts,GenomicRanges,GRangesList-method
> ###   pmapToTranscripts,GRangesList,GRangesList-method mapFromTranscripts
> ###   mapFromTranscripts,GenomicRanges,GenomicRanges-method
> ###   mapFromTranscripts,GenomicRanges,GRangesList-method
> ###   pmapFromTranscripts
> ###   pmapFromTranscripts,IntegerRanges,GenomicRanges-method
> ###   pmapFromTranscripts,IntegerRanges,GRangesList-method
> ###   pmapFromTranscripts,GenomicRanges,GenomicRanges-method
> ###   pmapFromTranscripts,GenomicRanges,GRangesList-method
> ### Keywords: methods utilities
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. Basic Use: Conversion between CDS and Exon coordinates and the
> ##    genome
> ## ---------------------------------------------------------------------
> 
> ## Gene "Dgkb" has ENTREZID "217480":
> library(org.Mm.eg.db)

> Dgkb_geneid <- get("Dgkb", org.Mm.egSYMBOL2EG)
> 
> ## The gene is on the positive strand, chromosome 12:
> library(TxDb.Mmusculus.UCSC.mm10.knownGene)
> txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
> tx_by_gene <- transcriptsBy(txdb, by="gene")
> Dgkb_transcripts <- tx_by_gene[[Dgkb_geneid]]
> Dgkb_transcripts  # all 7 Dgkb transcripts are on chr12, positive strand
GRanges object with 7 ranges and 2 metadata columns:
      seqnames            ranges strand |     tx_id              tx_name
         <Rle>         <IRanges>  <Rle> | <integer>          <character>
  [1]    chr12 37817726-37982010      + |     94103 ENSMUST00000222337.1
  [2]    chr12 37880174-38136840      + |     94104 ENSMUST00000221176.1
  [3]    chr12 37880337-38632119      + |     94105 ENSMUST00000220990.1
  [4]    chr12 37880547-38580923      + |     94106 ENSMUST00000221540.1
  [5]    chr12 37880705-38634239      + |     94107 ENSMUST00000040500.8
  [6]    chr12 37880716-38175084      + |     94108 ENSMUST00000221098.1
  [7]    chr12 38019180-38174661      + |     94111 ENSMUST00000220606.1
  -------
  seqinfo: 66 sequences (1 circular) from mm10 genome
> 
> ## To map coordinates from local CDS or exon space to genome 
> ## space use mapFromTranscripts().
> 
> ## When mapping CDS coordinates to genome space the 'transcripts'
> ## argument is the collection of CDS parts by transcript.
> coord <- GRanges("chr12", IRanges(4, width=1))
> ## Get the names of the transcripts in the gene:
> Dgkb_tx_names <- mcols(Dgkb_transcripts)$tx_name
> Dgkb_tx_names
[1] "ENSMUST00000222337.1" "ENSMUST00000221176.1" "ENSMUST00000220990.1"
[4] "ENSMUST00000221540.1" "ENSMUST00000040500.8" "ENSMUST00000221098.1"
[7] "ENSMUST00000220606.1"
> ## Use these names to isolate the region of interest:
> cds_by_tx <- cdsBy(txdb, "tx", use.names=TRUE)
> Dgkb_cds_by_tx <- cds_by_tx[intersect(Dgkb_tx_names, names(cds_by_tx))]
> ## Dgkb CDS parts grouped by transcript (no-CDS transcripts omitted):
> Dgkb_cds_by_tx
GRangesList object of length 4:
$ENSMUST00000222337.1
GRanges object with 1 range and 3 metadata columns:
      seqnames            ranges strand |    cds_id    cds_name exon_rank
         <Rle>         <IRanges>  <Rle> | <integer> <character> <integer>
  [1]    chr12 37981941-37982010      + |    166108        <NA>         2
  -------
  seqinfo: 66 sequences (1 circular) from mm10 genome

$ENSMUST00000221176.1
GRanges object with 9 ranges and 3 metadata columns:
      seqnames            ranges strand |    cds_id    cds_name exon_rank
         <Rle>         <IRanges>  <Rle> | <integer> <character> <integer>
  [1]    chr12 37981941-37982010      + |    166108        <NA>         2
  [2]    chr12 38084167-38084243      + |    166109        <NA>         3
  [3]    chr12 38087573-38087593      + |    166110        <NA>         4
  [4]    chr12 38100364-38100517      + |    166111        <NA>         5
  [5]    chr12 38114533-38114673      + |    166112        <NA>         6
  [6]    chr12 38120606-38120655      + |    166113        <NA>         7
  [7]    chr12 38124169-38124243      + |    166114        <NA>         8
  [8]    chr12 38127264-38127383      + |    166115        <NA>         9
  [9]    chr12 38136541-38136681      + |    166117        <NA>        10
  -------
  seqinfo: 66 sequences (1 circular) from mm10 genome

...
<2 more elements>
> lengths(Dgkb_cds_by_tx)  # nb of CDS parts per transcript
ENSMUST00000222337.1 ENSMUST00000221176.1 ENSMUST00000220990.1 
                   1                    9                   24 
ENSMUST00000040500.8 
                  24 
> ## A requirement for mapping from transcript space to genome space
> ## is that seqnames in 'x' match the names in 'transcripts'.
> names(Dgkb_cds_by_tx) <- rep(seqnames(coord), length(Dgkb_cds_by_tx))
> ## There are 6 results, one for each transcript.
> mapFromTranscripts(coord, Dgkb_cds_by_tx)
GRanges object with 4 ranges and 2 metadata columns:
      seqnames    ranges strand |     xHits transcriptsHits
         <Rle> <IRanges>  <Rle> | <integer>       <integer>
  [1]    chr12  37981944      + |         1               1
  [2]    chr12  37981944      + |         1               2
  [3]    chr12  37981944      + |         1               3
  [4]    chr12  37981944      + |         1               4
  -------
  seqinfo: 66 sequences from an unspecified genome; no seqlengths
> 
> ## To map exon coordinates to genome space the 'transcripts'
> ## argument is the collection of exon regions by transcript.
> coord <- GRanges("chr12", IRanges(100, width=1))
> ex_by_tx <- exonsBy(txdb, "tx", use.names=TRUE)
> Dgkb_ex_by_tx <- ex_by_tx[Dgkb_tx_names]
> names(Dgkb_ex_by_tx) <- rep(seqnames(coord), length(Dgkb_ex_by_tx))
> ## Again the output has 6 results, one for each transcript.
> mapFromTranscripts(coord, Dgkb_ex_by_tx)
GRanges object with 7 ranges and 2 metadata columns:
      seqnames    ranges strand |     xHits transcriptsHits
         <Rle> <IRanges>  <Rle> | <integer>       <integer>
  [1]    chr12  37817825      + |         1               1
  [2]    chr12  37880273      + |         1               2
  [3]    chr12  37981772      + |         1               3
  [4]    chr12  37880646      + |         1               4
  [5]    chr12  37880804      + |         1               5
  [6]    chr12  37880815      + |         1               6
  [7]    chr12  38019279      + |         1               7
  -------
  seqinfo: 66 sequences from an unspecified genome; no seqlengths
> 
> ## To go the reverse direction and map from genome space to
> ## local CDS or exon space, use mapToTranscripts().
> 
> ## Genomic position 37981944 maps to CDS position 4:
> coord <- GRanges("chr12", IRanges(37981944, width=1))
> mapToTranscripts(coord, Dgkb_cds_by_tx)
GRanges object with 4 ranges and 2 metadata columns:
      seqnames    ranges strand |     xHits transcriptsHits
         <Rle> <IRanges>  <Rle> | <integer>       <integer>
  [1]    chr12         4      + |         1               1
  [2]    chr12         4      + |         1               2
  [3]    chr12         4      + |         1               3
  [4]    chr12         4      + |         1               4
  -------
  seqinfo: 1 sequence from an unspecified genome
> 
> ## Genomic position 37880273 maps to exon position 100:
> coord <- GRanges("chr12", IRanges(37880273, width=1))
> mapToTranscripts(coord, Dgkb_ex_by_tx)
GRanges object with 1 range and 2 metadata columns:
      seqnames    ranges strand |     xHits transcriptsHits
         <Rle> <IRanges>  <Rle> | <integer>       <integer>
  [1]    chr12       100      + |         1               2
  -------
  seqinfo: 1 sequence from an unspecified genome
> 
> 
> ## The following examples use more than 2GB of memory, which is more
> ## than what 32-bit Windows can handle:
> is_32bit_windows <- .Platform$OS.type == "windows" &&
+                     .Platform$r_arch == "i386"
> if (!is_32bit_windows) {
+ ## ---------------------------------------------------------------------
+ ## B. Map sequence locations in exons to the genome
+ ## ---------------------------------------------------------------------
+ 
+ ## NAGNAG alternative splicing plays an essential role in biological
+ ## processes and represents a highly adaptable system for
+ ## posttranslational regulation of gene function. The majority of
+ ## NAGNAG studies largely focus on messenger RNA. A study by Sun,
+ ## Lin, and Yan (http://www.hindawi.com/journals/bmri/2014/736798/)
+ ## demonstrated that NAGNAG splicing is also operative in large
+ ## intergenic noncoding RNA (lincRNA). One finding of interest was
+ ## that linc-POLR3G-10 exhibited two NAGNAG acceptors located in two
+ ## distinct transcripts: TCONS_00010012 and TCONS_00010010.
+ 
+ ## Extract the exon coordinates of TCONS_00010012 and TCONS_00010010:
+ lincrna <- c("TCONS_00010012", "TCONS_00010010")
+ library(TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts)
+ txdb <- TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts
+ exons <- exonsBy(txdb, by="tx", use.names=TRUE)[lincrna]
+ exons
+ 
+ ## The two NAGNAG acceptors were identified in the upstream region of
+ ## the fourth and fifth exons located in TCONS_00010012.
+ ## Extract the sequences for transcript TCONS_00010012:
+ library(BSgenome.Hsapiens.UCSC.hg19)
+ genome <- BSgenome.Hsapiens.UCSC.hg19
+ exons_seq <- getSeq(genome, exons[[1]])
+ 
+ ## TCONS_00010012 has 4 exons:
+ exons_seq
+ 
+ ## The most common triplet among the lincRNA sequences was CAG. Identify
+ ## the location of this pattern in all exons.
+ cag_loc <- vmatchPattern("CAG", exons_seq)
+ 
+ ## Convert the first occurance of CAG in each exon back to genome
+ ## coordinates.
+ first_loc <- do.call(c, sapply(cag_loc, "[", 1, simplify=TRUE))
+ pmapFromTranscripts(first_loc, exons[[1]])
+ 
+ ## ---------------------------------------------------------------------
+ ## C. Map dbSNP variants to CDS or cDNA coordinates
+ ## ---------------------------------------------------------------------
+ 
+ ## The GIPR gene encodes a G-protein coupled receptor for gastric
+ ## inhibitory polypeptide (GIP). Originally GIP was identified to
+ ## inhibited gastric acid secretion and gastrin release but was later
+ ## demonstrated to stimulate insulin release in the presence of elevated
+ ## glucose.
+ 
+ ## In this example 5 SNPs located in the GIPR gene are mapped to cDNA
+ ## coordinates. A list of SNPs in GIPR can be downloaded from dbSNP or
+ ## NCBI.
+ rsids <- c("rs4803846", "rs139322374", "rs7250736", "rs7250754",
+            "rs9749185")
+ 
+ ## Extract genomic coordinates with a SNPlocs package.
+ library(SNPlocs.Hsapiens.dbSNP144.GRCh38)
+ snps <- snpsById(SNPlocs.Hsapiens.dbSNP144.GRCh38, rsids)
+ 
+ ## Gene regions of GIPR can be extracted from a TxDb package of
+ ## compatible build. The TxDb package uses Entrez gene identifiers
+ ## and GIPR is a gene symbol. Let's first lookup its Entrez gene ID.
+ library(org.Hs.eg.db)
+ GIPR_geneid <- get("GIPR", org.Hs.egSYMBOL2EG)
+ 
+ ## The transcriptsBy() extractor returns a range for each transcript that
+ ## includes the UTR and exon regions (i.e., cDNA).
+ library(TxDb.Hsapiens.UCSC.hg38.knownGene)
+ txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
+ tx_by_gene <- transcriptsBy(txdb, "gene")
+ GIPR_transcripts <- tx_by_gene[GIPR_geneid]
+ GIPR_transcripts  # all 8 GIPR transcripts are on chr19, positive strand
+ 
+ ## Before mapping, the chromosome names (seqlevels) in the two
+ ## objects must be harmonized. The style is NCBI for 'snps' and
+ ## UCSC for 'GIPR_transcripts'.
+ seqlevelsStyle(snps)
+ seqlevelsStyle(GIPR_transcripts)
+ 
+ ## Modify the style (and genome) in 'snps' to match 'GIPR_transcripts'.
+ seqlevelsStyle(snps) <- seqlevelsStyle(GIPR_transcripts)
+ 
+ ## The 'GIPR_transcripts' object is a GRangesList of length 1. This single
+ ## list element contains the cDNA range for 8 different transcripts. To
+ ## map to each transcript individually 'GIPR_transcripts' must be unlisted
+ ## before mapping.
+ 
+ ## Map all 5 SNPS to all 8 transcripts:
+ mapToTranscripts(snps, unlist(GIPR_transcripts))
+ 
+ ## Map the first SNP to transcript "ENST00000590918.5" and the second to
+ ## "ENST00000263281.7".
+ pmapToTranscripts(snps[1:2], unlist(GIPR_transcripts)[1:2])
+ 
+ ## The cdsBy() extractor returns CDS parts by gene or by transcript.
+ ## Extract the CDS parts for transcript "ENST00000263281.7".
+ cds <- cdsBy(txdb, "tx", use.names=TRUE)["ENST00000263281.7"]
+ cds
+ 
+ ## The 'cds' object is a GRangesList of length 1 containing the ranges of
+ ## all CDS parts for single transcript "ENST00000263281.7".
+ 
+ ## To map to the concatenated group of ranges leave 'cds' as a GRangesList.
+ mapToTranscripts(snps, cds)
+ 
+ ## Only the second SNP could be mapped. Unlisting the 'cds' object maps
+ ## the SNPs to the individual cds ranges (vs the concatenated range).
+ mapToTranscripts(snps[2], unlist(cds))
+ 
+ ## The location is the same because the SNP hit the first CDS part. If
+ ## the transcript were on the "-" strand the difference in concatenated
+ ## vs non-concatenated position would be more obvious.
+ 
+ ## Change strand:
+ strand(cds) <- strand(snps) <- "-"
+ mapToTranscripts(snps[2], unlist(cds))
+ }
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: ‘rtracklayer’

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    FileForFormat

Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh38’
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 1160638 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
  Attaching package: 'Biostrings'
  
  The following object is masked from 'package:base':
  
      strsplit
  
  Loading required package: BiocIO
  Loading required package: rtracklayer
  
  Attaching package: 'rtracklayer'
  
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* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL GenomicFeatures
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘GenomicFeatures’ ...
** 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 (GenomicFeatures)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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("GenomicFeatures") || stop("unable to load GenomicFeatures package")
Loading required package: GenomicFeatures
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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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: GenomicRanges
Loading required package: AnnotationDbi
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")'.

[1] TRUE
> GenomicFeatures:::.test()
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

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