Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:02:43 -0400 (Wed, 16 Oct 2019).
Package 1572/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
SplicingGraphs 1.24.0 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 |
Package: SplicingGraphs |
Version: 1.24.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SplicingGraphs.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SplicingGraphs_1.24.0.tar.gz |
StartedAt: 2019-10-16 05:12:28 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 05:19:12 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 404.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SplicingGraphs.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SplicingGraphs.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SplicingGraphs_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SplicingGraphs.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘1.24.0’ * 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-3.9-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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed plotTranscripts-methods 37.554 1.179 37.953 toy_data 22.285 0.097 22.452 countReads-methods 9.700 1.058 9.977 sgedges-methods 7.855 1.240 8.129 sgedgesByGene-methods 5.967 1.424 6.537 txpath-methods 6.009 1.191 6.205 bubbles-methods 6.131 1.038 6.239 SplicingGraphs-class 6.013 1.092 6.313 rsgedgesByGene-methods 5.963 1.134 6.033 sgraph-methods 5.000 1.358 5.320 assignReads 5.277 0.967 5.434 * 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-3.9-bioc/meat/SplicingGraphs.Rcheck/00check.log’ for details.
SplicingGraphs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SplicingGraphs ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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)
SplicingGraphs.Rcheck/tests/run_unitTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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, 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 -- Wed Oct 16 05:19:08 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 20.011 1.340 20.991
SplicingGraphs.Rcheck/SplicingGraphs-Ex.timings
name | user | system | elapsed | |
SplicingGraphs-class | 6.013 | 1.092 | 6.313 | |
SplicingGraphs-package | 0 | 0 | 0 | |
assignReads | 5.277 | 0.967 | 5.434 | |
bubbles-methods | 6.131 | 1.038 | 6.239 | |
countReads-methods | 9.700 | 1.058 | 9.977 | |
plotTranscripts-methods | 37.554 | 1.179 | 37.953 | |
rsgedgesByGene-methods | 5.963 | 1.134 | 6.033 | |
sgedges-methods | 7.855 | 1.240 | 8.129 | |
sgedgesByGene-methods | 5.967 | 1.424 | 6.537 | |
sgraph-methods | 5.000 | 1.358 | 5.320 | |
toy_data | 22.285 | 0.097 | 22.452 | |
txpath-methods | 6.009 | 1.191 | 6.205 | |