Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:25 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the getDEE2 package: - Please 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 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 772/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
getDEE2 1.4.0 (landing page) Mark Ziemann
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: getDEE2 |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:getDEE2.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings getDEE2_1.4.0.tar.gz |
StartedAt: 2022-04-12 07:36:35 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 07:42:09 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 334.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: getDEE2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:getDEE2.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings getDEE2_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/getDEE2.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘getDEE2/DESCRIPTION’ ... OK * this is package ‘getDEE2’ version ‘1.4.0’ * 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 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 ... 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 1.491 0.115 18.462 getDEE2 1.484 0.113 31.473 list_bundles 0.406 0.008 5.171 Tx2Gene 0.318 0.059 17.695 loadTxCounts 0.288 0.045 12.135 loadGeneCounts 0.266 0.032 10.744 loadQcMx 0.206 0.023 11.662 loadGeneInfo 0.197 0.020 11.186 se 0.183 0.025 9.889 loadFullMeta 0.181 0.020 10.926 loadSummaryMeta 0.172 0.014 10.442 loadTxInfo 0.157 0.020 12.184 srx_agg 0.137 0.014 10.762 getDEE2Metadata 0.089 0.013 6.086 queryDEE2 0.076 0.000 6.108 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-getDEE2.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 NOTE See ‘/home/biocbuild/bbs-3.14-bioc/meat/getDEE2.Rcheck/00check.log’ for details.
getDEE2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL getDEE2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-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("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, 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 > 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 871444 bytes (851 KB) ================================================== downloaded 851 KB trying URL 'http://dee2.io/cgi-bin/request.sh?org=ecoli&x=SRR1613487&x=SRR1613488' downloaded 155 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$GeneCounts) , 20624168 ) + }) Test passed 😀 > > > # A. thaliana bundle > x <- getDEE2_bundle("athaliana", "SRP058781",col="SRP_accession") trying URL 'http://dee2.io/huge/athaliana/' downloaded 408 KB trying URL 'http://dee2.io/huge/athaliana/SRP058781_NA.zip' Content type 'application/zip' length 4214382 bytes (4.0 MB) ================================================== downloaded 4.0 MB For more information about DEE2 QC metrics, visit https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md > > test_that("ath bundles work", { + expect_equal( nrow(assays(x)[[1]]) , 32833 ) + expect_equal( ncol(assays(x)[[1]]) , 32 ) + }) Test passed 🌈 > > > # check absent present > dat <- query_bundles("drerio",c("SRP131781","SRP055996","SRXXX"),col="SRP_accession") trying URL 'http://dee2.io/huge/drerio/' downloaded 161 KB > > test_that("dre bundle query", { + expect_equal( length(dat$absent) , 1 ) + expect_equal( length(dat$present) , 2 ) + }) Test passed 🎊 > > proc.time() user system elapsed 9.650 1.112 45.911
getDEE2.Rcheck/getDEE2-Ex.timings
name | user | system | elapsed | |
Tx2Gene | 0.318 | 0.059 | 17.695 | |
getDEE2 | 1.484 | 0.113 | 31.473 | |
getDEE2Metadata | 0.089 | 0.013 | 6.086 | |
getDEE2_bundle | 1.491 | 0.115 | 18.462 | |
list_bundles | 0.406 | 0.008 | 5.171 | |
loadFullMeta | 0.181 | 0.020 | 10.926 | |
loadGeneCounts | 0.266 | 0.032 | 10.744 | |
loadGeneInfo | 0.197 | 0.020 | 11.186 | |
loadQcMx | 0.206 | 0.023 | 11.662 | |
loadSummaryMeta | 0.172 | 0.014 | 10.442 | |
loadTxCounts | 0.288 | 0.045 | 12.135 | |
loadTxInfo | 0.157 | 0.020 | 12.184 | |
queryDEE2 | 0.076 | 0.000 | 6.108 | |
query_bundles | 0.326 | 0.028 | 4.051 | |
se | 0.183 | 0.025 | 9.889 | |
srx_agg | 0.137 | 0.014 | 10.762 | |