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This page was generated on 2021-06-22 12:06:16 -0400 (Tue, 22 Jun 2021).

CHECK results for SplicingGraphs on riesling1

To the developers/maintainers of the SplicingGraphs package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SplicingGraphs.git to
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raw results

Package 1786/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SplicingGraphs 1.33.0  (landing page)
H. Pag├Ęs
Snapshot Date: 2021-06-21 14:50:06 -0400 (Mon, 21 Jun 2021)
URL: https://git.bioconductor.org/packages/SplicingGraphs
Branch: master
Last Commit: 6f313b4
Last Changed Date: 2021-05-19 11:58:48 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: SplicingGraphs
Version: 1.33.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SplicingGraphs.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SplicingGraphs_1.33.0.tar.gz
StartedAt: 2021-06-22 02:14:39 -0400 (Tue, 22 Jun 2021)
EndedAt: 2021-06-22 02:25:23 -0400 (Tue, 22 Jun 2021)
EllapsedTime: 643.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: SplicingGraphs.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SplicingGraphs.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SplicingGraphs_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/SplicingGraphs.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SplicingGraphs/DESCRIPTION' ... OK
* this is package 'SplicingGraphs' version '1.33.0'
* 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 'D:/biocbuild/bbs-3.14-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
  'GenomicFeatures:::.collapse_df' '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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'SplicingGraphs-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SplicingGraphs-class
> ### Title: SplicingGraphs objects
> ### Aliases: class:GeneModel GeneModel-class class:SplicingGraphs
> ###   SplicingGraphs-class seqnames,GeneModel-method
> ###   strand,GeneModel-method seqinfo,GeneModel-method
> ###   isCircular<-,GeneModel-method length,SplicingGraphs-method
> ###   names,SplicingGraphs-method [,SplicingGraphs,ANY,ANY-method
> ###   [[,SplicingGraphs,ANY,ANY-method elementNROWS,SplicingGraphs-method
> ###   unlist,SplicingGraphs-method seqnames,SplicingGraphs-method
> ###   strand,SplicingGraphs-method seqinfo,SplicingGraphs-method
> ###   isCircular<-,SplicingGraphs-method show,SplicingGraphs-method
> ###   SplicingGraphs SplicingGraphs,GRangesList-method
> ###   SplicingGraphs,TxDb-method
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## 1. Load a toy gene model as a TxDb object
> ## ---------------------------------------------------------------------
> 
> library(GenomicFeatures)
> suppressWarnings(
+   toy_genes_txdb <- makeTxDbFromGFF(toy_genes_gff())
+ )
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> 
> ## ---------------------------------------------------------------------
> ## 2. Compute all the splicing graphs (1 graph per gene) and return them
> ##    in a SplicingGraphs object
> ## ---------------------------------------------------------------------
> 
> ## Extract the exons grouped by transcript:
> ex_by_tx <- exonsBy(toy_genes_txdb, by="tx", use.names=TRUE)
> 
> ## Extract the transcripts grouped by gene:
> tx_by_gn <- transcriptsBy(toy_genes_txdb, by="gene")
> 
> sg <- SplicingGraphs(ex_by_tx, tx_by_gn)
Warning in socketConnection(port = port, server = TRUE, blocking = TRUE,  :
  port 11594 cannot be opened
Error in socketConnection(port = port, server = TRUE, blocking = TRUE,  : 
  cannot open the connection
Calls: SplicingGraphs ... <Anonymous> -> <Anonymous> -> newSOCKnode -> socketConnection
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
plotTranscripts-methods 29.28   0.31   52.18
toy_data                15.01   0.00   15.02
countReads-methods       5.94   0.05   30.35
sgedges-methods          4.81   0.01   25.97
rsgedgesByGene-methods   3.94   0.02   25.11
sgedgesByGene-methods    3.67   0.03   25.50
assignReads              3.56   0.03   26.14
txpath-methods           3.52   0.00   25.61
SplicingGraphs-class     3.35   0.03   29.75
bubbles-methods          3.20   0.00   25.44
sgraph-methods           2.61   0.02   23.76
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbuild/bbs-3.14-bioc/meat/SplicingGraphs.Rcheck/00check.log'
for details.


Installation output

SplicingGraphs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SplicingGraphs_1.33.0.tar.gz && rm -rf SplicingGraphs.buildbin-libdir && mkdir SplicingGraphs.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SplicingGraphs.buildbin-libdir SplicingGraphs_1.33.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SplicingGraphs_1.33.0.zip && rm SplicingGraphs_1.33.0.tar.gz SplicingGraphs_1.33.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 45.5M    1  835k    0     0  3960k      0  0:00:11 --:--:--  0:00:11 3941k
 23 45.5M   23 10.9M    0     0  9246k      0  0:00:05  0:00:01  0:00:04 9239k
 51 45.5M   51 23.3M    0     0  10.5M      0  0:00:04  0:00:02  0:00:02 10.5M
 83 45.5M   83 37.9M    0     0  11.8M      0  0:00:03  0:00:03 --:--:-- 11.8M
100 45.5M  100 45.5M    0     0  12.3M      0  0:00:03  0:00:03 --:--:-- 12.3M

install for i386

* 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
  converting help for package 'SplicingGraphs'
    finding HTML links ... done
    SplicingGraphs-class                    html  
REDIRECT:topic	 class:GeneModel -> SplicingGraphs-class.html [ FAIL ]
REDIRECT:topic	 class:SplicingGraphs -> SplicingGraphs-class.html [ FAIL ]
REDIRECT:topic	 isCircular<-,GeneModel-method -> SplicingGraphs-class.html [ FAIL ]
REDIRECT:topic	 isCircular<-,SplicingGraphs-method -> SplicingGraphs-class.html [ FAIL ]
    SplicingGraphs-package                  html  
    TSPCsg                                  html  
    assignReads                             html  
    bubbles-methods                         html  
    countReads-methods                      html  
    plotTranscripts-methods                 html  
    rsgedgesByGene-methods                  html  
    sgedges-methods                         html  
    sgedgesByGene-methods                   html  
    sgraph-methods                          html  
    toy_data                                html  
    txpath-methods                          html  
REDIRECT:topic	 txweight<- -> txpath-methods.html [ FAIL ]
REDIRECT:topic	 txweight<-,SplicingGraphs-method -> txpath-methods.html [ FAIL ]
** 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

install for x64

* installing *source* package 'SplicingGraphs' ...
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
* MD5 sums
packaged installation of 'SplicingGraphs' as SplicingGraphs_1.33.0.zip
* DONE (SplicingGraphs)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'SplicingGraphs' successfully unpacked and MD5 sums checked

Tests output

SplicingGraphs.Rcheck/tests_i386/run_unitTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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

Attaching package: 'IRanges'

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

    windows

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 Jun 22 02:24:30 2021 
*********************************************** 
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 
  10.34    0.40   22.12 

SplicingGraphs.Rcheck/tests_x64/run_unitTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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

Attaching package: 'IRanges'

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

    windows

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 Jun 22 02:24:55 2021 
*********************************************** 
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 
  11.59    0.40   24.87 

Example timings

SplicingGraphs.Rcheck/examples_i386/SplicingGraphs-Ex.timings

nameusersystemelapsed

SplicingGraphs.Rcheck/examples_x64/SplicingGraphs-Ex.timings

nameusersystemelapsed
SplicingGraphs-class 3.35 0.0329.75
SplicingGraphs-package000
assignReads 3.56 0.0326.14
bubbles-methods 3.20 0.0025.44
countReads-methods 5.94 0.0530.35
plotTranscripts-methods29.28 0.3152.18
rsgedgesByGene-methods 3.94 0.0225.11
sgedges-methods 4.81 0.0125.97
sgedgesByGene-methods 3.67 0.0325.50
sgraph-methods 2.61 0.0223.76
toy_data15.01 0.0015.02
txpath-methods 3.52 0.0025.61