Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:53 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the SplicingGraphs package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SplicingGraphs.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1830/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SplicingGraphs 1.32.0 (landing page) H. Pagès
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
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: 2021-10-14 11:44:05 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:50:59 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 414.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SplicingGraphs.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### 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 44.372 1.524 44.596 toy_data 23.980 0.220 24.206 countReads-methods 8.565 1.224 8.321 sgedges-methods 7.094 1.501 6.741 sgedgesByGene-methods 5.540 2.081 5.242 SplicingGraphs-class 6.348 1.076 6.162 rsgedgesByGene-methods 4.984 1.408 4.711 assignReads 4.794 1.360 4.619 txpath-methods 4.414 1.413 4.383 bubbles-methods 4.370 1.237 4.157 * 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.
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)
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 Oct 14 11:50:56 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 17.337 1.034 17.836
SplicingGraphs.Rcheck/SplicingGraphs-Ex.timings
name | user | system | elapsed | |
SplicingGraphs-class | 6.348 | 1.076 | 6.162 | |
SplicingGraphs-package | 0.001 | 0.000 | 0.001 | |
assignReads | 4.794 | 1.360 | 4.619 | |
bubbles-methods | 4.370 | 1.237 | 4.157 | |
countReads-methods | 8.565 | 1.224 | 8.321 | |
plotTranscripts-methods | 44.372 | 1.524 | 44.596 | |
rsgedgesByGene-methods | 4.984 | 1.408 | 4.711 | |
sgedges-methods | 7.094 | 1.501 | 6.741 | |
sgedgesByGene-methods | 5.540 | 2.081 | 5.242 | |
sgraph-methods | 3.122 | 1.295 | 2.959 | |
toy_data | 23.980 | 0.220 | 24.206 | |
txpath-methods | 4.414 | 1.413 | 4.383 | |