Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:44 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 830/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicScores 2.14.1 (landing page) Robert Castelo
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the GenomicScores package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicScores.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: GenomicScores |
Version: 2.14.1 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GenomicScores.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GenomicScores_2.14.1.tar.gz |
StartedAt: 2023-11-02 10:50:50 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 10:56:17 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 327.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GenomicScores.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GenomicScores.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GenomicScores_2.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicScores.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicScores/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GenomicScores’ version ‘2.14.1’ * 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 ... NOTE Found the following hidden files and directories: inst/gscores-template/inst/extdata/.gitkeep These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GenomicScores’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘hdf5Backend’ * 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 ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘GenomicScores-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: gscores > ### Title: Accessing genomic gscores > ### Aliases: gscores,GScores,GenomicRanges-method > ### gscores,GScores,character-method gscores score,GScores-method > ### Keywords: utilities > > ### ** Examples > > ## one genomic range of width 5 > gr1 <- GRanges(seqnames="chr7", IRanges(start=117232380, width=5)) > gr1 GRanges object with 1 range and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr7 117232380-117232384 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths > > ## five genomic ranges of width 1 > gr2 <- GRanges(seqnames="chr7", IRanges(start=117232380:117232384, width=1)) > gr2 GRanges object with 5 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr7 117232380 * [2] chr7 117232381 * [3] chr7 117232382 * [4] chr7 117232383 * [5] chr7 117232384 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths > > ## accessing genomic gscores from an annotation package > if (require(phastCons100way.UCSC.hg19)) { + library(GenomicRanges) + + gsco <- phastCons100way.UCSC.hg19 + gsco + gscores(gsco, gr1) + score(gsco, gr1) + gscores(gsco, gr2) + populations(gsco) + gscores(gsco, gr2, pop="DP2") + } Loading required package: phastCons100way.UCSC.hg19 GRanges object with 5 ranges and 1 metadata column: seqnames ranges strand | DP2 <Rle> <IRanges> <Rle> | <numeric> [1] chr7 117232380 * | 0.81 [2] chr7 117232381 * | 0.81 [3] chr7 117232382 * | 0.99 [4] chr7 117232383 * | 0.99 [5] chr7 117232384 * | 0.98 ------- seqinfo: 93 sequences (1 circular) from Genome Reference Consortium GRCh37 genome > > if (require(MafDb.1Kgenomes.phase1.hs37d5)) { + mafdb <- MafDb.1Kgenomes.phase1.hs37d5 + mafdb + populations(mafdb) + + ## lookup allele frequencies for SNP rs1129038, located at 15:28356859, a + ## SNP associated to blue and brown eye colors as reported by Eiberg et al. + ## Blue eye color in humans may be caused by a perfectly associated founder + ## mutation in a regulatory element located within the HERC2 gene + ## inhibiting OCA2 expression. Human Genetics, 123(2):177-87, 2008 + ## [http://www.ncbi.nlm.nih.gov/pubmed/18172690] + gscores(mafdb, GRanges("15:28356859"), pop=populations(mafdb)) + gscores(mafdb, "rs1129038", pop=populations(mafdb)) + } Loading required package: MafDb.1Kgenomes.phase1.hs37d5 Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.1Kgenomes.phase1.hs37d5’ Loading first time annotations of identifiers to genomic positions, produced by data provider. * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicScores.Rcheck/00check.log’ for details.
GenomicScores.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL GenomicScores ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘GenomicScores’ ... ** 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 (GenomicScores)
GenomicScores.Rcheck/tests/runTests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" 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. > BiocGenerics:::testPackage("GenomicScores") 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 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'GenomicScores' The following object is masked from 'package:utils': citation Loading required package: phastCons100way.UCSC.hg19 RUNIT TEST PROTOCOL -- Thu Nov 2 10:56:14 2023 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicScores RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 Warning message: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'phastCons100way.UCSC.hg19' > > proc.time() user system elapsed 23.082 2.111 27.219
GenomicScores.Rcheck/GenomicScores-Ex.timings
name | user | system | elapsed | |
GScores-class | 15.955 | 2.557 | 19.693 | |
availableGScores | 2.304 | 2.218 | 8.840 | |