Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:09 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 1366/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MultiRNAflow 1.0.0 (landing page) Rodolphe Loubaton
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the MultiRNAflow package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MultiRNAflow.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: MultiRNAflow |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MultiRNAflow.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MultiRNAflow_1.0.0.tar.gz |
StartedAt: 2024-04-16 01:22:04 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 01:32:48 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 644.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MultiRNAflow.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MultiRNAflow.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MultiRNAflow_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MultiRNAflow.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘MultiRNAflow/DESCRIPTION’ ... OK * this is package ‘MultiRNAflow’ version ‘1.0.0’ * 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 ‘MultiRNAflow’ 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 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 ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DEanalysisTimeAndGroup 8.024 0.272 8.296 DEplotHeatmaps 6.769 0.223 6.992 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Running_analysis_with_MultiRNAflow.Rmd’ using ‘UTF-8’... OK ‘MultiRNAflow_vignette-knitr.Rnw’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
MultiRNAflow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MultiRNAflow ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘MultiRNAflow’ ... ** using staged installation ** R ** data ** 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 (MultiRNAflow)
MultiRNAflow.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(MultiRNAflow) Loading required package: Mfuzz Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: e1071 Attaching package: 'DynDoc' The following object is masked from 'package:BiocGenerics': path > > test_check("MultiRNAflow") converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode [1] "Preprocessing" [1] "Differential expression step with DESeq2::DESeq()" estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing [1] "Case 2 analysis : Biological conditions only" estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing [1] "DE time analysis for each biological condition." [1] "DE group analysis for each time measurement." [1] "Combined time and group results." [1] "DE time analysis for each biological condition." [1] "DE group analysis for each time measurement." [1] "Combined time and group results." estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing converting counts to integer mode 0 genes excluded. 1 genes excluded. 0 genes excluded. 1 genes excluded. 0 genes excluded. 3 genes excluded. 0 genes excluded. 4 genes excluded. 0 genes excluded. 3 genes excluded. 0 genes excluded. 4 genes excluded. 0 genes excluded. 3 genes excluded. 0 genes excluded. 4 genes excluded. 0 genes excluded. 3 genes excluded. 0 genes excluded. 4 genes excluded. converting counts to integer mode converting counts to integer mode converting counts to integer mode [ FAIL 0 | WARN 0 | SKIP 0 | PASS 197 ] > > proc.time() user system elapsed 89.556 2.841 92.395
MultiRNAflow.Rcheck/MultiRNAflow-Ex.timings
name | user | system | elapsed | |
CharacterNumbers | 0 | 0 | 0 | |
ColnamesToFactors | 0.012 | 0.002 | 0.014 | |
DATAnormalization | 1.109 | 0.063 | 1.173 | |
DATAplotBoxplotSamples | 1.398 | 0.089 | 1.487 | |
DATAplotExpression1Gene | 0.598 | 0.060 | 0.658 | |
DATAplotExpressionGenes | 1.057 | 0.076 | 1.133 | |
DATAprepSE | 0.203 | 0.000 | 0.203 | |
DEanalysisGlobal | 2.369 | 0.123 | 2.493 | |
DEanalysisGroup | 2.167 | 0.104 | 2.271 | |
DEanalysisSubData | 0.506 | 0.029 | 0.534 | |
DEanalysisTime | 3.902 | 0.163 | 4.065 | |
DEanalysisTimeAndGroup | 8.024 | 0.272 | 8.296 | |
DEplotAlluvial | 0.587 | 0.039 | 0.628 | |
DEplotBarplot | 0.291 | 0.015 | 0.307 | |
DEplotBarplotFacetGrid | 0.773 | 0.025 | 0.797 | |
DEplotBarplotTime | 0.237 | 0.000 | 0.237 | |
DEplotHeatmaps | 6.769 | 0.223 | 6.992 | |
DEplotVennBarplotGroup | 0.903 | 0.064 | 0.966 | |
DEplotVennBarplotTime | 0.975 | 0.029 | 1.003 | |
DEplotVolcanoMA | 2.700 | 0.067 | 2.768 | |
DEresultGroup | 1.980 | 0.085 | 2.064 | |
DEresultGroupPerTime | 3.220 | 0.099 | 3.320 | |
GSEAQuickAnalysis | 0.191 | 0.015 | 0.207 | |
GSEApreprocessing | 2.658 | 0.152 | 2.810 | |
HCPCanalysis | 2.069 | 0.052 | 2.121 | |
MFUZZanalysis | 1.528 | 0.108 | 1.637 | |
MFUZZclustersNumber | 0.580 | 0.023 | 0.604 | |
PCAanalysis | 1.708 | 0.028 | 1.737 | |
PCAgraphics | 0.986 | 0.052 | 1.039 | |
PCApreprocessing | 0.511 | 0.020 | 0.531 | |
PCArealization | 0.50 | 0.02 | 0.52 | |
RawCountsSimulation | 0.039 | 0.004 | 0.042 | |
RawCounts_Antoszewski2022_MOUSEsub500 | 0.003 | 0.000 | 0.004 | |
RawCounts_Leong2014_FISSIONsub500wt | 0.005 | 0.000 | 0.005 | |
RawCounts_Schleiss2021_CLLsub500 | 0.009 | 0.001 | 0.009 | |
RawCounts_Weger2021_MOUSEsub500 | 0.011 | 0.004 | 0.015 | |
Results_DEanalysis_sub500 | 0.084 | 0.004 | 0.088 | |