Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-22 11:36:15 -0400 (Wed, 22 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2056/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SplicingGraphs 1.44.0 (landing page) H. Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the SplicingGraphs package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: SplicingGraphs |
Version: 1.44.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SplicingGraphs.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SplicingGraphs_1.44.0.tar.gz |
StartedAt: 2024-05-22 06:59:03 -0400 (Wed, 22 May 2024) |
EndedAt: 2024-05-22 07:13:13 -0400 (Wed, 22 May 2024) |
EllapsedTime: 850.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SplicingGraphs.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SplicingGraphs.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SplicingGraphs_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SplicingGraphs.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'SplicingGraphs/DESCRIPTION' ... OK * this is package 'SplicingGraphs' version '1.44.0' * 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 whether package 'SplicingGraphs' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: '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 code 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 whether startup messages can be suppressed ... 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 '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 Rd file 'countReads-methods.Rd': '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 (user + system) or elapsed time > 5s user system elapsed plotTranscripts-methods 46.05 0.81 80.14 toy_data 24.73 0.14 24.92 countReads-methods 9.06 0.14 41.73 sgedgesByGene-methods 7.34 0.05 39.97 sgedges-methods 7.16 0.16 41.50 SplicingGraphs-class 7.06 0.24 38.91 txpath-methods 5.87 0.13 39.78 rsgedgesByGene-methods 5.79 0.08 38.14 assignReads 5.47 0.05 38.53 bubbles-methods 5.14 0.09 37.30 sgraph-methods 4.78 0.04 38.07 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'run_unitTests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs See 'F:/biocbuild/bbs-3.19-bioc/meat/SplicingGraphs.Rcheck/00check.log' for details.
SplicingGraphs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL SplicingGraphs ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'SplicingGraphs' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SplicingGraphs)
SplicingGraphs.Rcheck/tests/run_unitTests.Rout
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 > SplicingGraphs:::.test() Attaching package: 'txdbmaker' The following objects are masked from 'package:GenomicFeatures': UCSCFeatureDbTableSchema, browseUCSCtrack, getChromInfoFromBiomart, makeFDbPackageFromUCSC, makeFeatureDbFromUCSC, makePackageName, makeTxDb, makeTxDbFromBiomart, makeTxDbFromEnsembl, makeTxDbFromGFF, makeTxDbFromGRanges, makeTxDbFromUCSC, makeTxDbPackage, makeTxDbPackageFromBiomart, makeTxDbPackageFromUCSC, supportedMiRBaseBuildValues, supportedUCSCFeatureDbTables, supportedUCSCFeatureDbTracks, supportedUCSCtables 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 May 22 07:12:58 2024 *********************************************** 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 22.85 1.18 41.23
SplicingGraphs.Rcheck/SplicingGraphs-Ex.timings
name | user | system | elapsed | |
SplicingGraphs-class | 7.06 | 0.24 | 38.91 | |
SplicingGraphs-package | 0 | 0 | 0 | |
assignReads | 5.47 | 0.05 | 38.53 | |
bubbles-methods | 5.14 | 0.09 | 37.30 | |
countReads-methods | 9.06 | 0.14 | 41.73 | |
plotTranscripts-methods | 46.05 | 0.81 | 80.14 | |
rsgedgesByGene-methods | 5.79 | 0.08 | 38.14 | |
sgedges-methods | 7.16 | 0.16 | 41.50 | |
sgedgesByGene-methods | 7.34 | 0.05 | 39.97 | |
sgraph-methods | 4.78 | 0.04 | 38.07 | |
toy_data | 24.73 | 0.14 | 24.92 | |
txpath-methods | 5.87 | 0.13 | 39.78 | |