##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SplicingGraphs.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings SplicingGraphs_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/SplicingGraphs.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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 ‘/home/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 loading without being on the library search path ... 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 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 ...
  ‘SplicingGraphs.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/SplicingGraphs.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL SplicingGraphs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘SplicingGraphs’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’
Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’
Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’
Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’
** testing if installed package keeps a record of temporary installation path
* DONE (SplicingGraphs)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("SplicingGraphs") || stop("unable to load SplicingGraphs package")
Loading required package: SplicingGraphs
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 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")'.

Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


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

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

    rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
Loading required package: Rgraphviz
Loading required package: graph

Attaching package: 'graph'

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

    complement

Loading required package: grid

Attaching package: 'grid'

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

    pattern


Attaching package: 'Rgraphviz'

The following objects are masked from 'package:IRanges':

    from, to

The following objects are masked from 'package:S4Vectors':

    from, to

[1] TRUE
Warning messages:
1: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs' 
2: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs' 
> SplicingGraphs:::.test()
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK


RUNIT TEST PROTOCOL -- Tue Apr 11 00:22:21 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SplicingGraphs RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 17.735   1.330  18.597