H. Pagès
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/SplicingGraphs |
| Branch: RELEASE_3_10 |
| Last Commit: 42f49b4 |
| Last Changed Date: 2019-11-20 00:45:12 -0400 (Wed, 20 Nov 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:38:44 -0400 (Wed, 15 Apr 2020).
| Package 1647/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SplicingGraphs 1.26.1 H. Pagès
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: SplicingGraphs |
| Version: 1.26.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SplicingGraphs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SplicingGraphs_1.26.1.tar.gz |
| StartedAt: 2020-04-15 05:54:17 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:02:59 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 522.2 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 --install=check:SplicingGraphs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SplicingGraphs_1.26.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/SplicingGraphs.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.26.1’
* 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-3.10-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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 56.700 1.699 58.365
toy_data 31.441 0.279 32.304
countReads-methods 10.850 0.894 10.985
sgedges-methods 8.524 1.173 8.756
sgedgesByGene-methods 6.572 1.156 6.848
rsgedgesByGene-methods 6.395 1.136 6.539
SplicingGraphs-class 6.336 0.935 6.057
assignReads 6.212 0.949 6.255
txpath-methods 5.751 1.257 5.919
bubbles-methods 5.544 0.792 5.598
sgraph-methods 4.285 0.967 4.302
* 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-3.10-bioc/meat/SplicingGraphs.Rcheck/00check.log’
for details.
SplicingGraphs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SplicingGraphs ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)
SplicingGraphs.Rcheck/tests/run_unitTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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, 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
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
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: '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 -- Wed Apr 15 06:02:52 2020
***********************************************
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
21.494 1.319 22.268
SplicingGraphs.Rcheck/SplicingGraphs-Ex.timings
| name | user | system | elapsed | |
| SplicingGraphs-class | 6.336 | 0.935 | 6.057 | |
| SplicingGraphs-package | 0.000 | 0.000 | 0.001 | |
| assignReads | 6.212 | 0.949 | 6.255 | |
| bubbles-methods | 5.544 | 0.792 | 5.598 | |
| countReads-methods | 10.850 | 0.894 | 10.985 | |
| plotTranscripts-methods | 56.700 | 1.699 | 58.365 | |
| rsgedgesByGene-methods | 6.395 | 1.136 | 6.539 | |
| sgedges-methods | 8.524 | 1.173 | 8.756 | |
| sgedgesByGene-methods | 6.572 | 1.156 | 6.848 | |
| sgraph-methods | 4.285 | 0.967 | 4.302 | |
| toy_data | 31.441 | 0.279 | 32.304 | |
| txpath-methods | 5.751 | 1.257 | 5.919 | |