Package: SplicingGraphs

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SplicingGraphs_1.18.0.tar.gz

StartedAt: 2018-04-12 09:55:31 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:01:39 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 368.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SplicingGraphs.Rcheck

Warnings: 3

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SplicingGraphs_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SplicingGraphs.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SplicingGraphs/DESCRIPTION’ ... OK
* this is package ‘SplicingGraphs’ version ‘1.18.0’
* 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 ‘/Users/biocbuild/bbs-3.6-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'
  'GenomicFeatures:::.collapse_df' 'IRanges:::newCompressedList0'
  'IRanges:::regroupBySupergroup' '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'
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotTranscripts-methods 33.180  0.166  34.496
toy_data                16.215  0.043  16.517
countReads-methods       6.222  0.021   6.363
* 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: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/SplicingGraphs.Rcheck/00check.log’
for details.

* installing *source* package ‘SplicingGraphs’ ...
** R
** inst
** preparing 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
Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’
Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’
* DONE (SplicingGraphs)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

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: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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: '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 -- Thu Apr 12 10:01:36 2018 
*********************************************** 
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 
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 11.816   0.308  12.152 

name	user	system	elapsed
SplicingGraphs-class	3.618	0.044	3.701
SplicingGraphs-package	0.001	0.000	0.000
assignReads	4.039	0.018	4.098
bubbles-methods	2.953	0.011	2.995
countReads-methods	6.222	0.021	6.363
plotTranscripts-methods	33.180	0.166	34.496
rsgedgesByGene-methods	3.229	0.031	3.320
sgedges-methods	3.963	0.022	4.092
sgedgesByGene-methods	2.690	0.019	2.795
sgraph-methods	1.621	0.008	1.657
toy_data	16.215	0.043	16.517
txpath-methods	3.120	0.017	3.201