Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:35 -0000 (Wed, 01 Mar 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" | 4266 |
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To the developers/maintainers of the atena package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/atena.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 94/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
atena 1.5.4 (landing page) Beatriz Calvo-Serra
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: atena |
Version: 1.5.4 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:atena.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings atena_1.5.4.tar.gz |
StartedAt: 2023-02-27 20:48:00 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 20:54:08 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 368.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: atena.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:atena.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings atena_1.5.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/atena.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 ‘atena/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘atena’ version ‘1.5.4’ * 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 ‘atena’ 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotaTEs 12.019 0.912 37.778 rmskbasicparser 5.411 0.253 11.168 rmskidentity 4.984 0.228 7.900 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: 1 Test Suite : atena RUnit Tests - 13 test functions, 0 errors, 1 failure FAILURE in test_TEtranscripts: Error in checkEqualsNumeric(head(sort(assay(ttSE), decreasing = TRUE)), : Mean relative difference: 0.007380074 Test files with failing tests test_TEtranscripts.R test_TEtranscripts Error in BiocGenerics:::testPackage("atena") : unit tests failed for package atena Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘atena.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.17-bioc/meat/atena.Rcheck/00check.log’ for details.
atena.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL atena ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘atena’ ... ** 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 (atena)
atena.Rcheck/tests/runTests.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("atena") || stop("unable to load atena package") Loading required package: atena Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats 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 Loading required package: GenomicRanges 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: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians [1] TRUE > BiocGenerics:::testPackage("atena") | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% [1] "integer" [1] 149 122 Timing stopped at: 1.035 0.116 1.15 Error in checkEqualsNumeric(head(sort(assay(ttSE), decreasing = TRUE)), : Mean relative difference: 0.007380074 | | | 0% | |=================================== | 50% | |======================================================================| 100% Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand RUNIT TEST PROTOCOL -- Mon Feb 27 20:53:21 2023 *********************************************** Number of test functions: 13 Number of errors: 0 Number of failures: 1 1 Test Suite : atena RUnit Tests - 13 test functions, 0 errors, 1 failure FAILURE in test_TEtranscripts: Error in checkEqualsNumeric(head(sort(assay(ttSE), decreasing = TRUE)), : Mean relative difference: 0.007380074 Test files with failing tests test_TEtranscripts.R test_TEtranscripts Error in BiocGenerics:::testPackage("atena") : unit tests failed for package atena Execution halted
atena.Rcheck/atena-Ex.timings
name | user | system | elapsed | |
ERVmapParam-class | 0.159 | 0.004 | 0.166 | |
QuantifyParam-class | 0.051 | 0.000 | 0.051 | |
TEtranscriptsParam-class | 0.042 | 0.000 | 0.043 | |
TelescopeParam-class | 1.001 | 0.004 | 1.005 | |
annotaTEs | 12.019 | 0.912 | 37.778 | |
atenaParam-class | 0.162 | 0.008 | 0.170 | |
ovFunctions | 2.655 | 0.127 | 2.786 | |
qtex | 1.519 | 0.040 | 1.559 | |
rmskbasicparser | 5.411 | 0.253 | 11.168 | |
rmskidentity | 4.984 | 0.228 | 7.900 | |