Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-07-28 12:05 -0400 (Mon, 28 Jul 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4512 |
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 852/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
getDEE2 1.19.3 (landing page) Mark 0000-0002-7688-6974 Ziemann
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the getDEE2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/getDEE2.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: getDEE2 |
Version: 1.19.3 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:getDEE2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings getDEE2_1.19.3.tar.gz |
StartedAt: 2025-07-27 22:41:02 -0400 (Sun, 27 Jul 2025) |
EndedAt: 2025-07-27 22:49:33 -0400 (Sun, 27 Jul 2025) |
EllapsedTime: 510.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: getDEE2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:getDEE2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings getDEE2_1.19.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/getDEE2.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘getDEE2/DESCRIPTION’ ... OK * this is package ‘getDEE2’ version ‘1.19.3’ * 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 ‘getDEE2’ 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 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 loading without being on the library search path ... 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 ... NOTE srx_agg: no visible global function definition for ‘is’ Undefined global functions or variables: is Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 getDEE2_bundle 1.731 0.088 18.417 getDEE2 1.243 0.062 34.015 getDEE2Metadata 0.902 0.013 10.967 Tx2Gene 0.637 0.039 20.562 loadSummaryMeta 0.496 0.014 15.095 list_bundles 0.502 0.002 5.226 se 0.344 0.078 14.239 loadGeneInfo 0.398 0.021 13.922 loadGeneCounts 0.387 0.027 14.390 loadQcMx 0.375 0.024 14.075 srx_agg 0.316 0.033 14.701 loadFullMeta 0.317 0.020 14.128 loadTxInfo 0.305 0.015 15.725 loadTxCounts 0.294 0.021 13.109 queryDEE2 0.162 0.015 8.799 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-getDEE2.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/getDEE2.Rcheck/00check.log’ for details.
getDEE2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL getDEE2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘getDEE2’ ... ** this is package ‘getDEE2’ version ‘1.19.3’ ** using staged installation Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. ** 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 (getDEE2)
getDEE2.Rcheck/tests/test-getDEE2.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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("getDEE2") > library("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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors 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 Loading required package: Seqinfo 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 > library("testthat") > > # E. coli > x<-getDEE2("ecoli",c("SRR1613487","SRR1613488"),legacy=TRUE) trying URL 'http://dee2.io/metadata/ecoli_metadata.tsv.cut' Content type 'text/tab-separated-values' length 2078249 bytes (2.0 MB) ================================================== downloaded 2.0 MB trying URL 'http://dee2.io/cgi-bin/request.sh?org=ecoli&x=SRR1613487&x=SRR1613488' downloaded 154 KB For more information about DEE2 QC metrics, visit https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md > > test_that("eco works", { + expect_equal( sum(x$GeneCounts) , 20624168 ) + }) Test passed 🎉 > > > # A. thaliana bundle > x <- getDEE2_bundle("athaliana", "SRP058781",col="SRP_accession") trying URL 'http://dee2.io/huge/athaliana/' downloaded 753 KB trying URL 'http://dee2.io/huge/athaliana/SRP058781_NA.zip' Content type 'application/zip' length 4214382 bytes (4.0 MB) ================================================== downloaded 4.0 MB For more information about DEE2 QC metrics, visit https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md > > test_that("ath bundles work", { + expect_equal( nrow(assays(x)[[1]]) , 32833 ) + expect_equal( ncol(assays(x)[[1]]) , 32 ) + }) Test passed 🥇 > > > # check absent present > dat <- query_bundles("drerio",c("SRP131781","SRP055996","SRXXX"),col="SRP_accession") trying URL 'http://dee2.io/huge/drerio/' downloaded 170 KB > > test_that("dre bundle query", { + expect_equal( length(dat$absent) , 1 ) + expect_equal( length(dat$present) , 2 ) + }) Test passed 🌈 > > proc.time() user system elapsed 12.481 0.657 51.080
getDEE2.Rcheck/getDEE2-Ex.timings
name | user | system | elapsed | |
Tx2Gene | 0.637 | 0.039 | 20.562 | |
getDEE2 | 1.243 | 0.062 | 34.015 | |
getDEE2Metadata | 0.902 | 0.013 | 10.967 | |
getDEE2_bundle | 1.731 | 0.088 | 18.417 | |
list_bundles | 0.502 | 0.002 | 5.226 | |
loadFullMeta | 0.317 | 0.020 | 14.128 | |
loadGeneCounts | 0.387 | 0.027 | 14.390 | |
loadGeneInfo | 0.398 | 0.021 | 13.922 | |
loadQcMx | 0.375 | 0.024 | 14.075 | |
loadSummaryMeta | 0.496 | 0.014 | 15.095 | |
loadTxCounts | 0.294 | 0.021 | 13.109 | |
loadTxInfo | 0.305 | 0.015 | 15.725 | |
queryDEE2 | 0.162 | 0.015 | 8.799 | |
query_bundles | 0.535 | 0.004 | 4.954 | |
se | 0.344 | 0.078 | 14.239 | |
srx_agg | 0.316 | 0.033 | 14.701 | |