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 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 1268/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MIRit 1.3.0 (landing page) Jacopo Ronchi
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the MIRit package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MIRit.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: MIRit |
Version: 1.3.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MIRit.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MIRit_1.3.0.tar.gz |
StartedAt: 2024-12-23 23:52:26 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 23:56:35 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 249.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MIRit.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MIRit.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MIRit_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MIRit.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘MIRit/DESCRIPTION’ ... OK * this is package ‘MIRit’ version ‘1.3.0’ * 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 ‘MIRit’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 ... NOTE Unexported objects imported by ':::' calls: 'graphite:::convertEdges' 'graphite:::selectDb' See the note in ?`:::` about the use of this operator. * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: MirnaExperiment-class.Rd: DataFrame gseaPlot.Rd: ggplot2 Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 R/sysdata.rda ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/MIRit.Rcheck/00check.log’ for details.
MIRit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MIRit ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘MIRit’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c pathwayScore.cpp -o pathwayScore.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o MIRit.so RcppExports.o pathwayScore.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-MIRit/00new/MIRit/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MIRit)
MIRit.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 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. > # 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(MIRit) Loading required package: MultiAssayExperiment Loading required package: 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: 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 > > test_check("MIRit") Performing differential expression analysis with limma... Differential expression analysis reported 17 significant miRNAs with p < 0.05 (correction: fdr). You can use the 'mirnaDE()' function to access results. Performing differential expression analysis with edgeR... Differential expression analysis reported 5 significant miRNAs with p < 0.05 (correction: fdr). You can use the 'mirnaDE()' function to access results. Performing differential expression analysis with voom... Differential expression analysis reported 8 significant miRNAs with p < 0.05 (correction: fdr). You can use the 'mirnaDE()' function to access results. Performing differential expression analysis with limma... Differential expression analysis reported 3 significant miRNAs with p < 0.05 (correction: fdr). You can use the 'mirnaDE()' function to access results. Performing the enrichment of upregulated genes... Performing the enrichment of downregulated genes... The enrichment of genes reported 1 significantly enriched terms for downregulated genes and 0 for upregulated genes. Ranking genes based on signed.pval... Performing gene-set enrichment analysis (GSEA)... GSEA reported 10 significantly enriched terms. Performing Correlation Adjusted MEan RAnk gene set test (CAMERA)... CAMERA reported 2 significantly enriched terms. As specified by the user, a correlation will be used. Performing Spearman's correlation analysis... A statistically significant correlation between 3 miRNA-target pairs was found! As specified by the user, a association will be used. Performing One-sided Fisher's exact test... A statistically significant association between 5 DE-miRNAs and 6 genes was found! As specified by the user, a association will be used. Performing One-sided Fisher's exact test with Lancaster's mid-p correction... A statistically significant association between 5 DE-miRNAs and 6 genes was found! As specified by the user, a association will be used. Performing One-sided Boschloo's exact test... A statistically significant association between 2 DE-miRNAs and 1 genes was found! As specified by the user, a fry will be used. Performing miRNA-gene integrative analysis using 'fry' method... A statistically significant association between 2 DE-miRNAs and 4 genes was found! As specified by the user, a correlation will be used. Performing Spearman's correlation analysis... A statistically significant correlation between 169 miRNA-target pairs was found! Reading KEGG pathways from cache... Adding miRNA-gene interactions to biological pathways... Loading required namespace: graph Performing topological sorting of pathway nodes... Calculating pathway scores... Generating random permutations... Calculating p-values with 100 permutations... Correcting p-values through the max-T procedure... The topologically-aware integrative pathway analysis reported 3 significantly altered pathways! As specified by the user, a association will be used. Performing One-sided Fisher's exact test... A statistically significant association between 3 DE-miRNAs and 5 genes was found! As specified by the user, a fry will be used. Performing miRNA-gene integrative analysis using 'fry' method... A statistically significant association between 2 DE-miRNAs and 4 genes was found! [ FAIL 0 | WARN 0 | SKIP 12 | PASS 15 ] ══ Skipped tests (12) ══════════════════════════════════════════════════════════ • On Bioconductor (4): 'test-association.R:13:5', 'test-differential-expression.R:17:5', 'test-targets.R:3:5', 'test-targets.R:21:5' • On CRAN (2): 'test-topological-integration.R:23:5', 'test-utils.R:20:5' • empty test (6): 'test-AllClasses.R:1:1', 'test-differential-expression.R:1:1', 'test-differential-expression.R:33:1', 'test-differential-expression.R:47:1', 'test-enrichment.R:24:1', 'test-integration.R:1:1' [ FAIL 0 | WARN 0 | SKIP 12 | PASS 15 ] > > proc.time() user system elapsed 39.743 6.111 25.228
MIRit.Rcheck/MIRit-Ex.timings
name | user | system | elapsed | |
MirnaExperiment | 0.411 | 0.046 | 0.457 | |
addDifferentialExpression | 0.465 | 0.012 | 0.477 | |
augmentedPathways | 0.040 | 0.003 | 0.042 | |
batchCorrection | 0.282 | 0.002 | 0.285 | |
deAccessors | 0.001 | 0.000 | 0.000 | |
deAnalysis | 0 | 0 | 0 | |
enrichGenes | 0 | 0 | 0 | |
enrichTargets | 2.050 | 0.042 | 2.096 | |
enrichedFeatures | 0.016 | 0.000 | 0.017 | |
enrichmentBarplot | 0.215 | 0.000 | 0.215 | |
enrichmentDatabase | 0 | 0 | 0 | |
enrichmentDotplot | 0.363 | 0.012 | 0.375 | |
enrichmentMethod | 0 | 0 | 0 | |
enrichmentMetric | 0.000 | 0.000 | 0.001 | |
enrichmentResults | 0 | 0 | 0 | |
findMirnaSNPs | 0.000 | 0.001 | 0.000 | |
geneSet | 0 | 0 | 0 | |
getEvidence | 0.000 | 0.000 | 0.001 | |
getTargets | 0 | 0 | 0 | |
gseaPlot | 0.185 | 0.024 | 0.209 | |
gseaRidgeplot | 0.198 | 0.001 | 0.200 | |
integratedPathways | 0 | 0 | 0 | |
integration | 0.007 | 0.007 | 0.014 | |
integrationDatabase | 0.000 | 0.001 | 0.000 | |
integrationDotplot | 0.227 | 0.000 | 0.226 | |
listPathways | 0.918 | 0.018 | 1.768 | |
loadExamples | 0.001 | 0.000 | 0.000 | |
mirVariantPlot | 0 | 0 | 0 | |
mirnaIntegration | 3.235 | 0.337 | 3.155 | |
mirnaTargets | 0 | 0 | 0 | |
pairedSamples | 0.000 | 0.000 | 0.001 | |
plotCorrelation | 0.335 | 0.043 | 0.379 | |
plotDE | 0.285 | 0.028 | 0.314 | |
plotDimensions | 0.165 | 0.014 | 0.180 | |
plotVolcano | 0.162 | 0.002 | 0.163 | |
preparePathways | 0 | 0 | 0 | |
searchDisease | 0 | 0 | 0 | |
significantAccessors | 0 | 0 | 0 | |
supportedOrganisms | 0.001 | 0.002 | 0.003 | |
topologicalAnalysis | 0.001 | 0.000 | 0.000 | |
visualizeNetwork | 0.230 | 0.003 | 0.233 | |