############################################################################## ############################################################################## ### ### Running command: ### ### 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 ### ############################################################################## ############################################################################## * 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 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 | [1] chrX 601-630 + | 10 Dx2 1 1 [2] chrX 666-675 + | 12 Dx4 2 5 end_SSid [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 | [1] chrX 601-620 + | 9 Dx1 1 1 [2] chrX 651-700 + | 11 Dx3 2 4 end_SSid [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 | [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 [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 | [1] chrX 601-630 + | 10 Dx2 1 1 [2] chrX 651-700 + | 11 Dx3 2 4 end_SSid [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 | [1] chrX 11-50 + | 2 Ax2 1 1 end_SSid [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 | [1] chrX 11-40 + | 1 Ax1 1 1 [2] chrX 71-100 + | 3 Ax3 2 4 end_SSid [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 | [1] chrX 251-300 - | 23 Bx1 1 3 [2] chrX 201-230 - | 20 Bx2 2 6 end_SSid [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 | [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 [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 | [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 [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 | [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 [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 | [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 [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.