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This page was generated on 2021-09-24 15:05:58 -0400 (Fri, 24 Sep 2021).

CHECK results for SplicingGraphs on nebbiolo1

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raw results

Package 1830/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SplicingGraphs 1.32.0  (landing page)
H. Pagès
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/SplicingGraphs
git_branch: RELEASE_3_13
git_last_commit: 6066f74
git_last_commit_date: 2021-05-19 11:58:48 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: SplicingGraphs
Version: 1.32.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SplicingGraphs.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SplicingGraphs_1.32.0.tar.gz
StartedAt: 2021-09-23 11:42:14 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 11:49:09 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 414.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SplicingGraphs.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SplicingGraphs.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SplicingGraphs_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/SplicingGraphs.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SplicingGraphs/DESCRIPTION’ ... OK
* this is package ‘SplicingGraphs’ version ‘1.32.0’
* 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-3.13-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'
  '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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
plotTranscripts-methods 42.713  2.102  43.436
toy_data                22.658  0.116  22.776
countReads-methods       8.287  1.288   8.086
SplicingGraphs-class     6.202  1.176   6.048
sgedges-methods          6.042  1.135   5.875
sgedgesByGene-methods    5.136  1.774   4.870
rsgedgesByGene-methods   4.718  1.265   4.593
assignReads              4.177  1.182   4.090
txpath-methods           3.874  1.169   3.793
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/SplicingGraphs.Rcheck/00check.log’
for details.



Installation output

SplicingGraphs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL SplicingGraphs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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)

Tests output

SplicingGraphs.Rcheck/tests/run_unitTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
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, 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 -- Thu Sep 23 11:49:05 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 
 18.365   1.451  19.330 

Example timings

SplicingGraphs.Rcheck/SplicingGraphs-Ex.timings

nameusersystemelapsed
SplicingGraphs-class6.2021.1766.048
SplicingGraphs-package000
assignReads4.1771.1824.090
bubbles-methods3.8981.0923.726
countReads-methods8.2871.2888.086
plotTranscripts-methods42.713 2.10243.436
rsgedgesByGene-methods4.7181.2654.593
sgedges-methods6.0421.1355.875
sgedgesByGene-methods5.1361.7744.870
sgraph-methods2.7631.0752.588
toy_data22.658 0.11622.776
txpath-methods3.8741.1693.793