Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:30 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1934/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SplicingGraphs 1.39.0 (landing page) H. Pagès
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: SplicingGraphs |
Version: 1.39.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SplicingGraphs.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SplicingGraphs_1.39.0.tar.gz |
StartedAt: 2023-02-07 16:41:01 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 16:48:57 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 475.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: SplicingGraphs.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SplicingGraphs.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SplicingGraphs_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SplicingGraphs.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘SplicingGraphs/DESCRIPTION’ ... OK * this is package ‘SplicingGraphs’ version ‘1.39.0’ * 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-3.17-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' '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 ... ERROR Running examples in ‘SplicingGraphs-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: TSPCsg > ### Title: TSPC splicing graphs > ### Aliases: TSPCsg TSPC > > ### ** Examples > > ## Load SplicingGraphs object 'TSPCsg': > filepath <- system.file("extdata", "TSPCsg.rda", package="SplicingGraphs") > load(filepath) > TSPCsg SplicingGraphs object with 9 gene(s) and 33 transcript(s) > > ## 'TSPCsg' has 1 element per gene and 'names(sg)' gives the gene ids. > names(TSPCsg) [1] "BAI1" "CYB561" "DAPL1" "ITGB8" "KIAA0319L" "LGSN" [7] "MKRN3" "ST14" "TREM2" > > ## 1 splicing graph per gene. (Note that gene MUC16 was dropped > ## because transcripts T-4 and T-5 in this gene both have their > ## 2nd exon *inside* their 3rd exon. Splicing graph theory doesn't > ## apply in that case.) > > ## Extract the edges of a given graph: > TSPCsgedges <- sgedges(TSPCsg["LGSN"]) > TSPCsgedges DataFrame with 19 rows and 5 columns from to sgedge_id ex_or_in tx_id <character> <character> <character> <factor> <CharacterList> 1 R 1 LGSN:R,1 T-1,T-2,T-3,... 2 1 5 LGSN:1,5 ex T-1,T-4n 3 5 6 LGSN:5,6 in T-1,T-2,T-4n,... 4 6 8 LGSN:6,8 ex T-1,T-2,T-4n,... 5 8 11 LGSN:8,11 in T-1,T-2 ... ... ... ... ... ... 15 6 7 LGSN:6,7 ex T-3 16 7 9 LGSN:7,9 in T-3 17 9 10 LGSN:9,10 ex T-3,T-4n,T-5n 18 10 11 LGSN:10,11 in T-3,T-4n,T-5n 19 8 9 LGSN:8,9 in T-4n,T-5n > > ## Plot the graph for a given gene: > plot(TSPCsg["LGSN"]) # or 'plot(sgraph(TSPCsgedges))' > > ## The reads from all samples have been assigned to 'TSPCsg'. > ## Use countReads() to summarize by splicing graph edge: > counts <- countReads(TSPCsg) Killed * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ ERROR Running the tests in ‘tests/run_unitTests.R’ failed. Last 13 lines of output: 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 Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘SplicingGraphs.Rnw’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘SplicingGraphs.Rnw’ ... Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’ Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’ > sg <- SplicingGraphs(txdb) Warning in parallel::mccollect(wait = FALSE, timeout = 1) : 1 parallel job did not deliver a result When sourcing ‘SplicingGraphs.R’: Error: wrong args for environment subassignment Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘SplicingGraphs.Rnw’ using Sweave Loading required package: GenomicFeatures Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ 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, aperm, 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 Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’ Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’ Warning in parallel::mccollect(wait = FALSE, timeout = 1) : 1 parallel job did not deliver a result Error: processing vignette 'SplicingGraphs.Rnw' failed with diagnostics: chunk 5 (label = SplicingGraphs_constructor) Error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment --- failed re-building ‘SplicingGraphs.Rnw’ SUMMARY: processing the following file failed: ‘SplicingGraphs.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 3 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/SplicingGraphs.Rcheck/00check.log’ for details.
SplicingGraphs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SplicingGraphs ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 Attaching package: 'BiocGenerics' 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, aperm, 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 Killed
SplicingGraphs.Rcheck/SplicingGraphs-Ex.timings
name | user | system | elapsed | |
SplicingGraphs-class | 7.070 | 1.582 | 10.067 | |
SplicingGraphs-package | 0.001 | 0.000 | 0.001 | |