H. Pagès
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SplicingGraphs |
| Branch: master |
| Last Commit: 4d72c72 |
| Last Changed Date: 2019-03-04 13:39:51 -0400 (Mon, 04 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:07:26 -0400 (Tue, 09 Apr 2019).
| Package 1542/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SplicingGraphs 1.23.3 H. Pagès
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: SplicingGraphs |
| Version: 1.23.3 |
| 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_1.23.3.tar.gz |
| StartedAt: 2019-04-09 05:43:31 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:53:24 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 593.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SplicingGraphs.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### Running 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_1.23.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SplicingGraphs.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.23.3’
* 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-3.9-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'
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 58.354 3.715 60.273
toy_data 31.237 0.464 31.705
countReads-methods 16.654 3.949 18.061
sgedges-methods 11.305 2.614 12.441
rsgedgesByGene-methods 8.631 2.866 9.190
txpath-methods 7.956 2.788 8.472
assignReads 8.024 2.584 8.364
sgedgesByGene-methods 7.896 2.698 8.354
bubbles-methods 7.857 2.529 8.338
SplicingGraphs-class 6.054 2.487 6.087
sgraph-methods 4.552 2.212 4.651
* 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-3.9-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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, 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
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: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 -- Tue Apr 9 05:53:14 2019
***********************************************
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
23.816 3.163 25.546
SplicingGraphs.Rcheck/SplicingGraphs-Ex.timings
| name | user | system | elapsed | |
| SplicingGraphs-class | 6.054 | 2.487 | 6.087 | |
| SplicingGraphs-package | 0.000 | 0.000 | 0.001 | |
| assignReads | 8.024 | 2.584 | 8.364 | |
| bubbles-methods | 7.857 | 2.529 | 8.338 | |
| countReads-methods | 16.654 | 3.949 | 18.061 | |
| plotTranscripts-methods | 58.354 | 3.715 | 60.273 | |
| rsgedgesByGene-methods | 8.631 | 2.866 | 9.190 | |
| sgedges-methods | 11.305 | 2.614 | 12.441 | |
| sgedgesByGene-methods | 7.896 | 2.698 | 8.354 | |
| sgraph-methods | 4.552 | 2.212 | 4.651 | |
| toy_data | 31.237 | 0.464 | 31.705 | |
| txpath-methods | 7.956 | 2.788 | 8.472 | |