Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1215/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metaseqR2 1.18.0 (landing page) Panagiotis Moulos
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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 | |||||||||
To the developers/maintainers of the metaseqR2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaseqR2.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: metaseqR2 |
Version: 1.18.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metaseqR2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings metaseqR2_1.18.0.tar.gz |
StartedAt: 2024-12-20 03:17:08 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 03:27:09 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 601.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metaseqR2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metaseqR2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings metaseqR2_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/metaseqR2.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'metaseqR2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'metaseqR2' version '1.18.0' * 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 'metaseqR2' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 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 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 getUcscUtr: no visible binding for global variable 'customDir' Undefined global functions or variables: customDir * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/metaseqR2/libs/x64/metaseqR2.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed metaseqr2 8.00 1.54 17.16 statNoiseq 7.39 0.21 7.61 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.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: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/metaseqR2.Rcheck/00check.log' for details.
metaseqR2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL metaseqR2 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'metaseqR2' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pval.c -o pval.o pval.c: In function 'add_from_both_sides': pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable] 26 | double esttotalperlength = total/2; | ^~~~~~~~~~~~~~~~~ gcc -shared -s -static-libgcc -o metaseqR2.dll tmp.def pval.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-metaseqR2/00new/metaseqR2/libs/x64 ** 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 (metaseqR2)
metaseqR2.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 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. > BiocGenerics:::testPackage("metaseqR2") 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, saveRDS, setdiff, table, tapply, union, 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 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 Attaching package: 'limma' The following object is masked from 'package:DESeq2': plotMA The following object is masked from 'package:BiocGenerics': plotMA locfit 1.5-9.10 2024-06-24 Attaching package: 'metaseqR2' The following object is masked from 'package:limma': readTargets Downsampling counts... Estimating initial dispersion population... Estimating dispersions using log-likelihood... Running simulations... This procedure requires time... Please wait...Using Ensembl host https://jan2024.archive.ensembl.org 2024-12-20 03:26:42: Data processing started... Read counts file: imported custom data frame Conditions: G1, G2 Samples to include: G1_rep1, G1_rep2, G1_rep3, G2_rep1, G2_rep2, G2_rep3 Samples to exclude: none Requested contrasts: G1_vs_G2 Annotation: embedded Organism: mm10 Reference source: ensembl Count type: gene Analysis preset: all_basic Transcriptional level: gene Exon filters: none applied Gene filters: none applied Filter application: postnorm Normalization algorithm: edaseq Normalization arguments: within.which: loess between.which: full Statistical algorithm(s): edger, limma Statistical arguments: edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) limma: none Meta-analysis method: simes Multiple testing correction: BH Logarithmic transformation offset: 1 Analysis preset: all_basic Quality control plots: Figure format: png Output directory: F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpgnTWZW Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change Output scale(s): natural, log2 Output values: normalized Loading gene annotation... Saving gene model to F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpgnTWZW/data/gene_model.RData Removing genes with zero counts in all samples... Normalizing with: edaseq Running statistical tests with: edger Contrast: G1_vs_G2 Running statistical tests with: limma Contrast: G1_vs_G2 Performing meta-analysis with simes Building output files... Contrast: G1_vs_G2 Adding non-filtered data... binding annotation... binding p-values... binding FDRs... binding meta p-values... binding adjusted meta p-values... binding natural normalized fold changes... binding log2 normalized fold changes... Writing output... 2024-12-20 03:26:42: Data processing finished! Total processing time: 00 seconds Estimating AUFC weights... Please wait... Processing edger Processing limma Retrieving edger Retrieving limma 2024-12-20 03:26:43: Data processing started... Read counts file: imported custom data frame Conditions: e14.5, adult_8_weeks Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2 Samples to exclude: none Requested contrasts: adult_8_weeks_vs_e14.5 Library sizes: e14.5_1: 3102907 e14.5_2: 2067905 a8w_1: 3742059 a8w_2: 4403954 Annotation: embedded Organism: mm9 Reference source: ensembl Count type: gene Analysis preset: medium_basic Transcriptional level: gene Exon filters: minActiveExons minActiveExons: exonsPerGene: 5 minExons: 2 frac: 0.2 Gene filters: length, avgReads, expression, biotype length: length: 500 avgReads: averagePerBp: 100 quantile: 0.25 expression: median: TRUE mean: FALSE quantile: NA known: NA custom: NA biotype: pseudogene: FALSE snRNA: FALSE protein_coding: FALSE antisense: FALSE miRNA: FALSE lincRNA: FALSE snoRNA: FALSE processed_transcript: FALSE misc_RNA: FALSE rRNA: TRUE sense_overlapping: FALSE sense_intronic: FALSE polymorphic_pseudogene: FALSE non_coding: FALSE three_prime_overlapping_ncrna: FALSE IG_C_gene: FALSE IG_J_gene: FALSE IG_D_gene: FALSE IG_V_gene: FALSE ncrna_host: FALSE Filter application: postnorm Normalization algorithm: edger Normalization arguments: method: TMM logratioTrim: 0.3 sumTrim: 0.05 doWeighting: TRUE Acutoff: -1e+10 p: 0.75 Statistical algorithm(s): edger, limma Statistical arguments: edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) limma: none Meta-analysis method: simes Multiple testing correction: BH p-value threshold: 0.05 Logarithmic transformation offset: 1 Analysis preset: medium_basic Quality control plots: mds Figure format: png Output directory: F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpgnTWZW Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change Output scale(s): natural, log2 Output values: normalized Loading gene annotation... Saving gene model to F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpgnTWZW/data/gene_model.RData Removing genes with zero counts in all samples... Normalizing with: edger Applying gene filter length... Threshold below which ignored: 500 Applying gene filter avgReads... Threshold below which ignored: 0.0659629215631332 Applying gene filter expression... Threshold below which ignored: 68 Applying gene filter biotype... Biotypes ignored: rRNA 2106 genes filtered out 1681 genes remain after filtering Running statistical tests with: edger Contrast: adult_8_weeks_vs_e14.5 Contrast adult_8_weeks_vs_e14.5: found 906 genes Running statistical tests with: limma Contrast: adult_8_weeks_vs_e14.5 Contrast adult_8_weeks_vs_e14.5: found 911 genes Performing meta-analysis with simes Building output files... Contrast: adult_8_weeks_vs_e14.5 Adding non-filtered data... binding annotation... binding p-values... binding FDRs... binding meta p-values... binding adjusted meta p-values... binding natural normalized fold changes... binding log2 normalized fold changes... Writing output... Adding filtered data... binding annotation... binding p-values... binding FDRs... binding meta p-values... binding adjusted meta p-values... binding natural normalized fold changes... binding log2 normalized fold changes... Writing output... Adding report data... binding annotation... binding meta p-values... binding adjusted meta p-values... binding log2 normalized fold changes... binding normalized mean counts... binding normalized mean counts... Creating quality control graphs... Plotting in png format... Plotting mds... Importing mds... Writing plot database in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpgnTWZW/data/reportdb.js Creating HTML report... Compressing figures... adding: biocbuild/bbs-3.20-bioc/tmpdir/RtmpgnTWZW/plots/qc/mds.png (deflated 49%) Downloading required JavaScript libraries...trying URL 'https://raw.github.com/HubSpot/pace/v1.0.0/pace.min.js' Content type 'text/plain; charset=utf-8' length 12363 bytes (12 KB) ================================================== downloaded 12 KB trying URL 'https://code.highcharts.com/highcharts.js' downloaded 268 KB trying URL 'https://code.highcharts.com/highcharts-more.js' downloaded 92 KB trying URL 'https://code.highcharts.com/modules/exporting.js' downloaded 19 KB trying URL 'https://code.highcharts.com/modules/offline-exporting.js' downloaded 26 KB trying URL 'https://code.highcharts.com/modules/export-data.js' downloaded 12 KB trying URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js' Content type 'application/javascript' length 35122 bytes (34 KB) ================================================== downloaded 34 KB trying URL 'http://jvenn.toulouse.inrae.fr/app/js/jvenn.min.js' Content type 'application/javascript' length 100524 bytes (98 KB) ================================================== downloaded 98 KB trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js' downloaded 55 KB processing file: metaseqr2_report.Rmd output file: metaseqr2_report.knit.md "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc188d02b6e4ede.html --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" +RTS -K2048m -RTS --variable "material:true" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:true" --variable "cards:true" --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template "F:\biocbuild\bbs-3.20-bioc\R\library\rmdformats\templates\material\material.html" --highlight-style kate --variable theme=bootstrap --include-in-header "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpgnTWZW\rmarkdown-str188d0341a185d.html" Output created: F:/biocbuild/bbs-3.20-bioc/tmpdir/RtmpgnTWZW/index.html 2024-12-20 03:26:55: Data processing finished! Total processing time: 12 seconds RUNIT TEST PROTOCOL -- Fri Dec 20 03:26:55 2024 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : metaseqR2 RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 There were 50 or more warnings (use warnings() to see the first 50) > > proc.time() user system elapsed 32.81 3.12 40.71
metaseqR2.Rcheck/metaseqR2-Ex.timings
name | user | system | elapsed | |
buildAnnotationDatabase | 0 | 0 | 0 | |
buildCustomAnnotation | 0 | 0 | 0 | |
combineBonferroni | 0 | 0 | 0 | |
combineHarmonic | 0.00 | 0.00 | 0.03 | |
combineMaxp | 0 | 0 | 0 | |
combineMinp | 0 | 0 | 0 | |
combineSimes | 0 | 0 | 0 | |
combineWeight | 0 | 0 | 0 | |
createSignalTracks | 0 | 0 | 0 | |
diagplotAvgFtd | 0.11 | 0.00 | 0.11 | |
diagplotBoxplot | 2.42 | 0.05 | 2.47 | |
diagplotCor | 0.18 | 0.02 | 0.19 | |
diagplotDeHeatmap | 1.03 | 0.06 | 1.10 | |
diagplotEdaseq | 0.51 | 0.10 | 0.62 | |
diagplotFiltered | 0.05 | 0.00 | 0.05 | |
diagplotFtd | 0.02 | 0.01 | 0.03 | |
diagplotMds | 0.18 | 0.00 | 0.19 | |
diagplotNoiseq | 0.43 | 0.16 | 0.58 | |
diagplotPairs | 0.81 | 0.08 | 0.89 | |
diagplotRoc | 0.03 | 0.04 | 0.08 | |
diagplotVenn | 0.31 | 0.05 | 0.43 | |
diagplotVolcano | 1.97 | 0.05 | 2.02 | |
downsampleCounts | 0.20 | 0.00 | 0.21 | |
estimateAufcWeights | 1.13 | 0.03 | 1.15 | |
estimateSimParams | 0.83 | 0.11 | 0.94 | |
getAnnotation | 2.46 | 0.21 | 4.50 | |
getDefaults | 0 | 0 | 0 | |
getInstalledAnnotations | 0 | 0 | 0 | |
getWeights | 0 | 0 | 0 | |
importCustomAnnotation | 1.44 | 0.03 | 1.49 | |
loadAnnotation | 0 | 0 | 0 | |
makeSimDataSd | 1.14 | 0.08 | 1.22 | |
makeSimDataTcc | 3.23 | 0.07 | 3.32 | |
metaTest | 0 | 0 | 0 | |
metaseqr2 | 8.00 | 1.54 | 17.16 | |
metaseqrPlot | 0.83 | 0.06 | 0.89 | |
normalizeAbsseq | 0.91 | 0.14 | 1.05 | |
normalizeDeseq | 0.22 | 0.08 | 0.29 | |
normalizeDeseq2 | 0.57 | 0.03 | 0.61 | |
normalizeDss | 0.27 | 0.01 | 0.28 | |
normalizeEdaseq | 0.34 | 0.05 | 0.40 | |
normalizeEdger | 0.11 | 0.06 | 0.17 | |
normalizeNbpseq | 0.14 | 0.03 | 0.17 | |
normalizeNoiseq | 0.21 | 0.02 | 0.23 | |
read2count | 2.49 | 0.30 | 4.32 | |
readTargets | 0.03 | 0.01 | 0.20 | |
statAbsseq | 1.47 | 0.08 | 1.55 | |
statDeseq | 1.36 | 0.02 | 1.37 | |
statDeseq2 | 4.44 | 0.03 | 4.47 | |
statDss | 0.93 | 0.02 | 0.95 | |
statEdger | 0.80 | 0.01 | 0.81 | |
statLimma | 0.37 | 0.00 | 0.38 | |
statNbpseq | 1.52 | 0.04 | 1.54 | |
statNoiseq | 7.39 | 0.21 | 7.61 | |