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### Running command:
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### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SplicingGraphs.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SplicingGraphs_1.38.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/SplicingGraphs.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SplicingGraphs/DESCRIPTION' ... OK
* this is package 'SplicingGraphs' version '1.38.0'
* 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 whether package 'SplicingGraphs' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
See 'F:/biocbuild/bbs-3.16-bioc/meat/SplicingGraphs.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'GenomicFeatures' 'GenomicAlignments' 'Rgraphviz' 'igraph'
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'igraph' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
'S4Vectors:::matchIntegerPairs' 'S4Vectors:::orderIntegerPairs'
'S4Vectors:::selfmatchIntegerPairs'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'BiocGenerics:::testPackage' 'GenomicAlignments:::fillJunctionGaps'
'IRanges:::newCompressedList0' 'IRanges:::regroupBySupergroup'
'IRanges:::unlist_as_integer' 'S4Vectors:::setPrototypeFromObject'
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 ... WARNING
Undocumented code objects:
'reportReads'
Undocumented S4 methods:
generic '[' and siglist 'SplicingGraphs,ANY,ANY,ANY'
generic 'reportReads' and siglist 'SplicingGraphs'
generic 'updateObject' and siglist 'SplicingGraphs'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'countReads-methods':
'reportReads'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'SplicingGraphs-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rsgedgesByGene-methods
> ### Title: Extract the reduced edges and their ranges from a SplicingGraphs
> ### object
> ### Aliases: rsgedgesByGene-methods uninformativeSSids
> ### uninformativeSSids,ANY-method uninformativeSSids,DataFrame-method
> ### rsgedgesByTranscript rsgedgesByTranscript,SplicingGraphs-method
> ### rsgedgesByGene rsgedgesByGene,SplicingGraphs-method rsgedges sgedges2
> ### rsgraph sgraph2
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## 1. Make SplicingGraphs object 'sg' from toy gene model (see
> ## '?SplicingGraphs')
> ## ---------------------------------------------------------------------
> example(SplicingGraphs)
SplcnG> ## ---------------------------------------------------------------------
SplcnG> ## 1. Load a toy gene model as a TxDb object
SplcnG> ## ---------------------------------------------------------------------
SplcnG>
SplcnG> library(GenomicFeatures)
SplcnG> suppressWarnings(
SplcnG+ toy_genes_txdb <- makeTxDbFromGFF(toy_genes_gff())
SplcnG+ )
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
SplcnG> ## ---------------------------------------------------------------------
SplcnG> ## 2. Compute all the splicing graphs (1 graph per gene) and return them
SplcnG> ## in a SplicingGraphs object
SplcnG> ## ---------------------------------------------------------------------
SplcnG>
SplcnG> ## Extract the exons grouped by transcript:
SplcnG> ex_by_tx <- exonsBy(toy_genes_txdb, by="tx", use.names=TRUE)
SplcnG> ## Extract the transcripts grouped by gene:
SplcnG> tx_by_gn <- transcriptsBy(toy_genes_txdb, by="gene")
SplcnG> sg <- SplicingGraphs(ex_by_tx, tx_by_gn)
SplcnG> sg
SplicingGraphs object with 5 gene(s) and 13 transcript(s)
SplcnG> ## Alternatively 'sg' can be constructed directly from the TxDb
SplcnG> ## object:
SplcnG> sg2 <- SplicingGraphs(toy_genes_txdb) # same as 'sg'
SplcnG> sg2
SplicingGraphs object with 5 gene(s) and 13 transcript(s)
SplcnG> ## Note that because SplicingGraphs objects have a slot that is an
SplcnG> ## environment (for caching the bubbles), they cannot be compared with
SplcnG> ## 'identical()' (will always return FALSE). 'all.equal()' should be
SplcnG> ## used instead:
SplcnG> stopifnot(isTRUE(all.equal(sg2, sg)))
SplcnG> ## 'sg' has 1 element per gene and 'names(sg)' gives the gene ids:
SplcnG> length(sg)
[1] 5
SplcnG> names(sg)
[1] "geneA" "geneB" "geneC" "geneD" "geneE"
SplcnG> ## ---------------------------------------------------------------------
SplcnG> ## 3. Basic manipulation of a SplicingGraphs object
SplcnG> ## ---------------------------------------------------------------------
SplcnG>
SplcnG> ## Basic accessors:
SplcnG> seqnames(sg)
geneA geneB geneC geneD geneE
chrX chrX chrX chrX chrX
Levels: chrX
SplcnG> strand(sg)
geneA geneB geneC geneD geneE
+ - + + +
Levels: + - *
SplcnG> seqinfo(sg)
Seqinfo object with 1 sequence from an unspecified genome; no seqlengths:
seqnames seqlengths isCircular genome
chrX NA NA <NA>
SplcnG> ## Number of transcripts per gene:
SplcnG> elementNROWS(sg)
geneA geneB geneC geneD geneE
2 2 3 4 2
SplcnG> ## The transcripts of a given gene can be extracted with [[. The result
SplcnG> ## is an *unnamed* GRangesList object containing the exons grouped by
SplcnG> ## transcript:
SplcnG> sg[["geneD"]]
GRangesList object of length 4:
[[1]]
GRanges object with 2 ranges and 5 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank start_SSid
<Rle> <IRanges> <Rle> | <integer> <character> <integer> <integer>
[1] chrX 601-630 + | 10 Dx2 1 1
[2] chrX 666-675 + | 12 Dx4 2 5
end_SSid
<integer>
[1] 3
[2] 6
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
[[2]]
GRanges object with 2 ranges and 5 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank start_SSid
<Rle> <IRanges> <Rle> | <integer> <character> <integer> <integer>
[1] chrX 601-620 + | 9 Dx1 1 1
[2] chrX 651-700 + | 11 Dx3 2 4
end_SSid
<integer>
[1] 2
[2] 8
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
[[3]]
GRanges object with 3 ranges and 5 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank start_SSid
<Rle> <IRanges> <Rle> | <integer> <character> <integer> <integer>
[1] chrX 601-620 + | 9 Dx1 1 1
[2] chrX 666-675 + | 12 Dx4 2 5
[3] chrX 691-700 + | 13 Dx5 3 7
end_SSid
<integer>
[1] 2
[2] 6
[3] 8
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
[[4]]
GRanges object with 2 ranges and 5 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank start_SSid
<Rle> <IRanges> <Rle> | <integer> <character> <integer> <integer>
[1] chrX 601-630 + | 10 Dx2 1 1
[2] chrX 651-700 + | 11 Dx3 2 4
end_SSid
<integer>
[1] 3
[2] 8
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
SplcnG> ## See '?plotTranscripts' for how to plot those transcripts.
SplcnG>
SplcnG> ## The transcripts of all the genes can be extracted with unlist(). The
SplcnG> ## result is a *named* GRangesList object containing the exons grouped
SplcnG> ## by transcript. The names on the object are the gene ids:
SplcnG> ex_by_tx <- unlist(sg)
SplcnG> ex_by_tx
GRangesList object of length 13:
$geneA
GRanges object with 1 range and 5 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank start_SSid
<Rle> <IRanges> <Rle> | <integer> <character> <integer> <integer>
[1] chrX 11-50 + | 2 Ax2 1 1
end_SSid
<integer>
[1] 3
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
$geneA
GRanges object with 2 ranges and 5 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank start_SSid
<Rle> <IRanges> <Rle> | <integer> <character> <integer> <integer>
[1] chrX 11-40 + | 1 Ax1 1 1
[2] chrX 71-100 + | 3 Ax3 2 4
end_SSid
<integer>
[1] 2
[2] 5
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
$geneB
GRanges object with 2 ranges and 5 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank start_SSid
<Rle> <IRanges> <Rle> | <integer> <character> <integer> <integer>
[1] chrX 251-300 - | 23 Bx1 1 3
[2] chrX 201-230 - | 20 Bx2 2 6
end_SSid
<integer>
[1] 1
[2] 4
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
...
<10 more elements>
> sg
SplicingGraphs object with 5 gene(s) and 13 transcript(s)
>
> ## 'sg' has 1 element per gene and 'names(sg)' gives the gene ids.
> names(sg)
[1] "geneA" "geneB" "geneC" "geneD" "geneE"
>
> ## ---------------------------------------------------------------------
> ## 2. rsgedgesByGene()
> ## ---------------------------------------------------------------------
> edges_by_gene <- rsgedgesByGene(sg)
> edges_by_gene
GRangesList object of length 5:
$geneA
GRanges object with 2 ranges and 5 metadata columns:
seqnames ranges strand | from to rsgedge_id
<Rle> <IRanges> <Rle> | <character> <character> <character>
[1] chrX 11-50 + | 1 3 geneA:1,3
[2] chrX 11-100 + | 1 5 geneA:1,2,4,5
ex_or_in tx_id
<factor> <CharacterList>
[1] ex A1
[2] mixed A2
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
$geneB
GRanges object with 5 ranges and 5 metadata columns:
seqnames ranges strand | from to rsgedge_id ex_or_in
<Rle> <IRanges> <Rle> | <character> <character> <character> <factor>
[1] chrX 251-300 - | 1 3 geneB:1,3 ex
[2] chrX 231-250 - | 3 4 geneB:3,4 in
[3] chrX 201-230 - | 4 6 geneB:4,6 ex
[4] chrX 251-270 - | 2 3 geneB:2,3 ex
[5] chrX 216-230 - | 4 5 geneB:4,5 ex
tx_id
<CharacterList>
[1] B1
[2] B1,B2
[3] B1
[4] B2
[5] B2
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
$geneC
GRanges object with 5 ranges and 5 metadata columns:
seqnames ranges strand | from to rsgedge_id
<Rle> <IRanges> <Rle> | <character> <character> <character>
[1] chrX 401-415 + | 1 2 geneC:1,2
[2] chrX 416-480 + | 2 8 geneC:2,7,8
[3] chrX 416-480 + | 2 9 geneC:2,5,6,9
[4] chrX 481-500 + | 9 10 geneC:9,10
[5] chrX 421-480 + | 3 9 geneC:3,4,9
ex_or_in tx_id
<factor> <CharacterList>
[1] ex C1,C2
[2] mixed C1
[3] mixed C2
[4] ex C2,C3
[5] mixed C3
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
...
<2 more elements>
> ## 'edges_by_gene' has the length and names of 'sg', that is, the names
> ## on it are the gene ids and are guaranteed to be unique.
>
> ## Extract the reduced edges and their ranges for a given gene:
> edges_by_gene[["geneA"]]
GRanges object with 2 ranges and 5 metadata columns:
seqnames ranges strand | from to rsgedge_id
<Rle> <IRanges> <Rle> | <character> <character> <character>
[1] chrX 11-50 + | 1 3 geneA:1,3
[2] chrX 11-100 + | 1 5 geneA:1,2,4,5
ex_or_in tx_id
<factor> <CharacterList>
[1] ex A1
[2] mixed A2
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
> ## Note that edge with global reduced edge id "geneA:1,2,4,5" is a mixed
> ## edge obtained by combining together edges "geneA:1,2" (exon),
> ## "geneA:2,4" (intron), and "geneA:4,5" (exon), during the graph
> ## reduction.
>
> stopifnot(identical(edges_by_gene["geneB"], rsgedgesByGene(sg["geneB"])))
>
> ## ---------------------------------------------------------------------
> ## 3. sgedgesByTranscript()
> ## ---------------------------------------------------------------------
> #edges_by_tx <- rsgedgesByTranscript(sg) # not ready yet!
> #edges_by_tx
>
> ## ---------------------------------------------------------------------
> ## 4. rsgedges(), rsgraph(), uninformativeSSids()
> ## ---------------------------------------------------------------------
> plot(sgraph(sg["geneB"]))
> uninformativeSSids(sg["geneB"])
[1] "1" "6" "2" "5"
>
> plot(rsgraph(sg["geneB"]))
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'plot': error in evaluating the argument 'self' in selecting a method for function 'nodeDataDefaults': multiple edges are not supported in graphNEL graphs
Calls: plot ... nodeDataDefaults -> .igraph.to.graphNEL2 -> igraph.to.graphNEL
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'run_unitTests.R'
OK
* 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: 1 ERROR, 3 WARNINGs, 2 NOTEs
See
'F:/biocbuild/bbs-3.16-bioc/meat/SplicingGraphs.Rcheck/00check.log'
for details.