Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
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 855/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
getDEE2 1.14.0 (landing page) Mark Ziemann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | 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: 1.14.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:getDEE2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings getDEE2_1.14.0.tar.gz |
StartedAt: 2024-06-12 23:33:18 -0400 (Wed, 12 Jun 2024) |
EndedAt: 2024-06-12 23:41:48 -0400 (Wed, 12 Jun 2024) |
EllapsedTime: 510.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: getDEE2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:getDEE2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings getDEE2_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/getDEE2.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘getDEE2/DESCRIPTION’ ... OK * this is package ‘getDEE2’ version ‘1.14.0’ * 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 ‘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 1.692 0.093 21.071 getDEE2 1.377 0.096 31.648 getDEE2Metadata 0.826 0.384 11.161 Tx2Gene 0.556 0.047 22.311 loadQcMx 0.392 0.028 13.988 loadGeneInfo 0.374 0.031 13.438 loadSummaryMeta 0.358 0.034 13.760 srx_agg 0.337 0.020 13.095 loadGeneCounts 0.327 0.024 13.585 loadFullMeta 0.314 0.031 17.677 se 0.314 0.024 13.138 loadTxCounts 0.310 0.020 14.216 loadTxInfo 0.311 0.005 13.832 queryDEE2 0.186 0.023 8.995 * 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-3.19-bioc/meat/getDEE2.Rcheck/00check.log’ for details.
getDEE2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL getDEE2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘getDEE2’ ... ** 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 (getDEE2)
getDEE2.Rcheck/tests/test-getDEE2.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 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 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 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: 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 > 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 2078161 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$GeneCounts) , 20624168 ) + }) Test passed 🎊 > > > # A. thaliana bundle > x <- getDEE2_bundle("athaliana", "SRP058781",col="SRP_accession") trying URL 'http://dee2.io/huge/athaliana/' downloaded 461 KB trying URL 'http://dee2.io/huge/athaliana/SRP058781_NA.zip' Content type 'application/zip' length 4214382 bytes (4.0 MB) ================================================== downloaded 4.0 MB For more information about DEE2 QC metrics, visit https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md > > test_that("ath bundles work", { + expect_equal( nrow(assays(x)[[1]]) , 32833 ) + expect_equal( ncol(assays(x)[[1]]) , 32 ) + }) Test passed 🥇 > > > # check absent present > dat <- query_bundles("drerio",c("SRP131781","SRP055996","SRXXX"),col="SRP_accession") trying URL 'http://dee2.io/huge/drerio/' downloaded 161 KB > > test_that("dre bundle query", { + expect_equal( length(dat$absent) , 1 ) + expect_equal( length(dat$present) , 2 ) + }) Test passed 🌈 > > proc.time() user system elapsed 12.072 1.031 50.985
getDEE2.Rcheck/getDEE2-Ex.timings
name | user | system | elapsed | |
Tx2Gene | 0.556 | 0.047 | 22.311 | |
getDEE2 | 1.377 | 0.096 | 31.648 | |
getDEE2Metadata | 0.826 | 0.384 | 11.161 | |
getDEE2_bundle | 1.692 | 0.093 | 21.071 | |
list_bundles | 0.527 | 0.000 | 4.273 | |
loadFullMeta | 0.314 | 0.031 | 17.677 | |
loadGeneCounts | 0.327 | 0.024 | 13.585 | |
loadGeneInfo | 0.374 | 0.031 | 13.438 | |
loadQcMx | 0.392 | 0.028 | 13.988 | |
loadSummaryMeta | 0.358 | 0.034 | 13.760 | |
loadTxCounts | 0.310 | 0.020 | 14.216 | |
loadTxInfo | 0.311 | 0.005 | 13.832 | |
queryDEE2 | 0.186 | 0.023 | 8.995 | |
query_bundles | 0.382 | 0.000 | 4.908 | |
se | 0.314 | 0.024 | 13.138 | |
srx_agg | 0.337 | 0.020 | 13.095 | |