Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:34 -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 txcutr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/txcutr.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 2096/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
txcutr 1.5.0 (landing page) Mervin Fansler
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: txcutr |
Version: 1.5.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:txcutr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings txcutr_1.5.0.tar.gz |
StartedAt: 2023-02-07 18:25:29 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 18:32:24 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 415.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: txcutr.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:txcutr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings txcutr_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/txcutr.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 ‘txcutr/DESCRIPTION’ ... OK * this is package ‘txcutr’ version ‘1.5.0’ * 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 ‘txcutr’ 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 dependencies in R code ... OK * 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 ‘txcutr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: exportFASTA > ### Title: Export Transcriptome as FASTA > ### Aliases: exportFASTA > > ### ** Examples > > library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene) 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")'. > library(BSgenome.Scerevisiae.UCSC.sacCer3) Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: rtracklayer > > ## load annotation and genome > txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene > sacCer3 <- BSgenome.Scerevisiae.UCSC.sacCer3 > > ## restrict to 'chrI' transcripts (makes for briefer example runtime) > seqlevels(txdb) <- c("chrI") > > ## last 500 nts per tx > txdb_w500 <- truncateTxome(txdb) 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Warning in parallel::mccollect(wait = FALSE, timeout = 1) : 1 parallel job did not deliver a result Error in reducer$value.cache[[as.character(idx)]] <- values : wrong args for environment subassignment Calls: truncateTxome ... .bploop_impl -> .collect_result -> .reducer_add -> .reducer_add Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘intro.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘intro.Rmd’ using rmarkdown Quitting from lines 118-123 (intro.Rmd) Error: processing vignette 'intro.Rmd' failed with diagnostics: wrong args for environment subassignment --- failed re-building ‘intro.Rmd’ SUMMARY: processing the following file failed: ‘intro.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs See ‘/home/biocbuild/bbs-3.17-bioc/meat/txcutr.Rcheck/00check.log’ for details.
txcutr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL txcutr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘txcutr’ ... ** using staged installation ** R ** 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 (txcutr)
txcutr.Rcheck/tests/testthat.Rout
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. > library(testthat) > library(txcutr) > > test_check("txcutr") Loading required package: stats4 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 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: 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")'. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 1 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 1 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 1 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 1 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 117 ] > > proc.time() user system elapsed 95.967 15.044 111.167
txcutr.Rcheck/txcutr-Ex.timings
name | user | system | elapsed |