Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 226/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BloodGen3Module 1.15.0 (landing page) Darawan Rinchai
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
To the developers/maintainers of the BloodGen3Module package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BloodGen3Module.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: BloodGen3Module |
Version: 1.15.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BloodGen3Module.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BloodGen3Module_1.15.0.tar.gz |
StartedAt: 2024-12-23 22:44:08 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:50:12 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 363.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BloodGen3Module.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BloodGen3Module.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BloodGen3Module_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/BloodGen3Module.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'BloodGen3Module/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BloodGen3Module' version '1.15.0' * 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 whether package 'BloodGen3Module' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module' Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module' Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module' Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module' See 'E:/biocbuild/bbs-3.21-bioc/meat/BloodGen3Module.Rcheck/00install.out' for details. * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 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 R/sysdata.rda ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Groupcomparison 25.74 3.69 30.56 gridplot 21.17 1.92 23.21 fingerprintplot 11.00 1.12 11.72 Groupcomparisonlimma 9.48 1.12 10.77 Individualcomparison 9.43 0.68 10.28 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test-fold_change.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See 'E:/biocbuild/bbs-3.21-bioc/meat/BloodGen3Module.Rcheck/00check.log' for details.
BloodGen3Module.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL BloodGen3Module ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'BloodGen3Module' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module' Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module' Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module' Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module' Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module' Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module' Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module' ** testing if installed package can be loaded from final location Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module' Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module' Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module' Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module' ** testing if installed package keeps a record of temporary installation path * DONE (BloodGen3Module)
BloodGen3Module.Rcheck/tests/test-fold_change.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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("gtools") > library("testthat") > library("BloodGen3Module") Warning messages: 1: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module' 2: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module' 3: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module' 4: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module' > > fold_change = function(df_raw = df_raw, + sample_info = sample_info, + Group_column = Group_column, + Test_group=Test_group, + Ref_group=Ref_group){ + + FC.group = data.frame(matrix(ncol = 1, nrow = nrow(df_raw))) + colnames(FC.group) = Test_group + rownames(FC.group) = rownames(df_raw) + + for (k in 1:nrow(df_raw)) { + signature = rownames(df_raw)[k] + test.table <- sample_info + test.table$scores <- df_raw[k,] + T2 <- test.table[test.table[, Group_column]==Test_group,] # "Group_test"; the selected column could be changed to your interested group comparison + T1 <- test.table[test.table[, Group_column]==Ref_group,] # "Group_test"; the selected column could be changed to your interested group comparison + FC.group[signature,] <- foldchange(mean(T2$scores),mean(T1$scores)) + } + FCgroup <- data.frame(FC.group) + } > > > library(ExperimentHub) 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: AnnotationHub Loading required package: BiocFileCache Loading required package: dbplyr > 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: 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 The following object is masked from 'package:ExperimentHub': cache The following object is masked from 'package:AnnotationHub': cache > dat = ExperimentHub() > res = query(dat , "GSE13015") > GSE13015 = res[["EH5429"]] GSE13015 not installed. Full functionality, documentation, and loading of data might not be possible without installing loading from cache > data_matrix = assay(GSE13015) > sample_ann = data.frame(colData(GSE13015)) > > > test_that("test fold_change", { + a = FCgroup = fold_change(df_raw = data_matrix[c(1:5),], + sample_info = sample_ann, + Group_column = "Group_test", + Test_group="Sepsis", + Ref_group="Control") + b = FCgroup = fold_change(df_raw = data_matrix[c(1:5),], + sample_info = sample_ann, + Group_column = "Group_test", + Test_group="Sepsis", + Ref_group="Control") + + expect_that(a, equals(b)) + }) Test passed 🎉 > > proc.time() user system elapsed 17.01 2.92 20.28
BloodGen3Module.Rcheck/BloodGen3Module-Ex.timings
name | user | system | elapsed | |
Groupcomparison | 25.74 | 3.69 | 30.56 | |
Groupcomparisonlimma | 9.48 | 1.12 | 10.77 | |
Individualcomparison | 9.43 | 0.68 | 10.28 | |
fingerprintplot | 11.00 | 1.12 | 11.72 | |
fold_change | 2.14 | 0.38 | 2.68 | |
gridplot | 21.17 | 1.92 | 23.21 | |