Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-11 11:46 -0400 (Mon, 11 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 1340/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mosdef 1.4.1 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the mosdef package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mosdef.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: mosdef |
Version: 1.4.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mosdef.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mosdef_1.4.1.tar.gz |
StartedAt: 2025-08-09 03:09:57 -0400 (Sat, 09 Aug 2025) |
EndedAt: 2025-08-09 03:22:47 -0400 (Sat, 09 Aug 2025) |
EllapsedTime: 770.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mosdef.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mosdef.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mosdef_1.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/mosdef.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mosdef/DESCRIPTION’ ... OK * this is package ‘mosdef’ version ‘1.4.1’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘mosdef’ 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 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 run_topGO 123.537 5.965 129.655 run_goseq 82.301 5.107 89.881 run_cluPro 49.033 2.427 51.648 gene_plot 5.422 0.158 5.663 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/mosdef.Rcheck/00check.log’ for details.
mosdef.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mosdef ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘mosdef’ ... ** this is package ‘mosdef’ version ‘1.4.1’ ** 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 (mosdef)
mosdef.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library("testthat") > library("mosdef") > > test_check("mosdef") Loading required package: S4Vectors 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 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: GenomicRanges Loading required package: GenomeInfoDb 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: 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 Loading required package: graph Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: SparseM groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Attaching package: 'topGO' The following object is masked from 'package:IRanges': members using counts and average transcript lengths from tximeta 'select()' returned 1:many mapping between keys and columns estimating size factors using 'avgTxLength' from assays(dds), correcting for library size estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing 'select()' returned 1:many mapping between keys and columns estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns Your dataset has 36 DE genes. You selected 36 (100.00%) genes for the enrichment analysis. You are analyzing up_and_down-regulated genes in the `res_de` container Your dataset has 36 DE genes. You selected 36 (100.00%) genes for the enrichment analysis. You are analyzing up_and_down-regulated genes in the `res_de` container Can't find hg38/ensGene length data in genLenDataBase... Found the annotation package, TxDb.Hsapiens.UCSC.hg38.knownGene Trying to get the gene lengths from it. Loading required package: GenomicFeatures Attaching package: 'GenomicFeatures' The following object is masked from 'package:topGO': genes Fetching GO annotations... Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns Your dataset has 36 DE genes. You selected 36 (100.00%) genes for the enrichment analysis. You are analyzing up_and_down-regulated genes in the `res_de` container 153 GO terms were analyzed. Not all of them are significantly enriched. We suggest further subsetting the output list by for example: using a pvalue cutoff in the column: 'p.value_elim'. 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns using 'avgTxLength' from assays(dds), correcting for library size Could not find the specified gene (`SPARCL1`) in the `res_de` object. Still, the general HTML content has been generated. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 104 ] > > proc.time() user system elapsed 108.003 5.869 115.760
mosdef.Rcheck/mosdef-Ex.timings
name | user | system | elapsed | |
buttonifier | 0.351 | 0.040 | 0.402 | |
create_link_ENSEMBL | 0.195 | 0.006 | 0.201 | |
create_link_GO | 0.000 | 0.000 | 0.001 | |
create_link_GTEX | 0.405 | 0.012 | 0.417 | |
create_link_HPA | 0.240 | 0.006 | 0.246 | |
create_link_NCBI | 0.245 | 0.006 | 0.258 | |
create_link_UniProt | 0.394 | 0.006 | 0.400 | |
create_link_dbPTM | 0.227 | 0.005 | 0.233 | |
create_link_genecards | 0.220 | 0.005 | 0.225 | |
create_link_pubmed | 0.223 | 0.006 | 0.228 | |
de_table_painter | 0.668 | 0.054 | 0.738 | |
de_volcano | 1.925 | 0.100 | 2.127 | |
deresult_to_df | 0.270 | 0.015 | 0.386 | |
dot-info_enrichrun | 0 | 0 | 0 | |
gene_plot | 5.422 | 0.158 | 5.663 | |
geneinfo_to_html | 0.005 | 0.001 | 0.007 | |
get_annotation_orgdb | 3.338 | 0.130 | 3.473 | |
get_expr_values | 4.047 | 0.131 | 4.180 | |
go_to_html | 0.108 | 0.015 | 0.125 | |
go_volcano | 3.220 | 0.602 | 3.829 | |
map_to_color | 0.577 | 0.016 | 0.595 | |
mosdef_de_container_check | 2.485 | 0.114 | 2.606 | |
mosdef_res_check | 0.174 | 0.008 | 0.183 | |
pair_corr | 3.001 | 0.154 | 3.160 | |
plot_ma | 2.273 | 0.118 | 2.392 | |
run_cluPro | 49.033 | 2.427 | 51.648 | |
run_goseq | 82.301 | 5.107 | 89.881 | |
run_topGO | 123.537 | 5.965 | 129.655 | |
styleColorBar_divergent | 0.067 | 0.015 | 0.083 | |