Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-12 12:07 -0500 (Thu, 12 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" | 4739 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4482 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4510 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4462 |
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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metaseqR2_1.18.0.tar.gz |
StartedAt: 2024-12-10 05:37:09 -0500 (Tue, 10 Dec 2024) |
EndedAt: 2024-12-10 06:05:39 -0500 (Tue, 10 Dec 2024) |
EllapsedTime: 1710.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metaseqR2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metaseqR2_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/metaseqR2.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * 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 for sufficient/correct file permissions ... OK * checking whether package ‘metaseqR2’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed statNoiseq 16.460 0.092 17.161 read2count 13.244 1.753 17.891 statDeseq2 7.315 0.106 7.583 metaseqr2 5.697 0.623 315.538 buildCustomAnnotation 5.153 0.206 71.375 makeSimDataTcc 3.700 0.071 33.478 getAnnotation 1.702 0.083 68.927 estimateAufcWeights 1.259 0.087 5.401 createSignalTracks 1.187 0.110 86.806 diagplotVenn 0.170 0.016 10.354 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/metaseqR2.Rcheck/00check.log’ for details.
metaseqR2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metaseqR2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘metaseqR2’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pval.c -o pval.o pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable] double esttotalperlength = total/2; ^ 1 warning generated. clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o metaseqR2.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-metaseqR2/00new/metaseqR2/libs ** 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 ** 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 (metaseqR2)
metaseqR2.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > 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: '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 2024-12-10 06:05:05: 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: /tmp/RtmpIjruFl 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 /tmp/RtmpIjruFl/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... 2024-12-10 06:05:06: Data processing finished! Total processing time: 01 seconds Estimating AUFC weights... Please wait... Processing edger Processing limma Retrieving edger Retrieving limma 2024-12-10 06:05:07: 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: /tmp/RtmpIjruFl 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 /tmp/RtmpIjruFl/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 /tmp/RtmpIjruFl/data/reportdb.js Creating HTML report... Compressing figures... adding: tmp/RtmpIjruFl/plots/qc/mds.png (deflated 48%) 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 /usr/local/bin/pandoc +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/tmp/RtmpIjruFl/index.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmdformats/templates/material/material.html --highlight-style kate --variable theme=bootstrap --include-in-header /tmp/RtmpIjruFl/rmarkdown-stre02129ab65fb.html Output created: /private/tmp/RtmpIjruFl/index.html 2024-12-10 06:05:19: Data processing finished! Total processing time: 12 seconds RUNIT TEST PROTOCOL -- Tue Dec 10 06:05:19 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 53.296 3.523 61.521
metaseqR2.Rcheck/metaseqR2-Ex.timings
name | user | system | elapsed | |
buildAnnotationDatabase | 0.000 | 0.001 | 0.001 | |
buildCustomAnnotation | 5.153 | 0.206 | 71.375 | |
combineBonferroni | 0.001 | 0.000 | 0.001 | |
combineHarmonic | 0.002 | 0.002 | 3.590 | |
combineMaxp | 0.000 | 0.000 | 0.001 | |
combineMinp | 0 | 0 | 0 | |
combineSimes | 0.001 | 0.000 | 0.001 | |
combineWeight | 0.001 | 0.000 | 0.001 | |
createSignalTracks | 1.187 | 0.110 | 86.806 | |
diagplotAvgFtd | 0.074 | 0.008 | 0.081 | |
diagplotBoxplot | 0.728 | 0.020 | 0.747 | |
diagplotCor | 0.163 | 0.019 | 4.105 | |
diagplotDeHeatmap | 1.030 | 0.036 | 1.066 | |
diagplotEdaseq | 0.416 | 0.067 | 0.483 | |
diagplotFiltered | 0.024 | 0.009 | 0.032 | |
diagplotFtd | 0.023 | 0.009 | 0.033 | |
diagplotMds | 0.296 | 0.009 | 0.305 | |
diagplotNoiseq | 0.593 | 0.050 | 0.643 | |
diagplotPairs | 0.546 | 0.055 | 1.761 | |
diagplotRoc | 0.023 | 0.008 | 0.031 | |
diagplotVenn | 0.170 | 0.016 | 10.354 | |
diagplotVolcano | 1.626 | 0.070 | 1.696 | |
downsampleCounts | 0.289 | 0.001 | 0.291 | |
estimateAufcWeights | 1.259 | 0.087 | 5.401 | |
estimateSimParams | 1.198 | 0.035 | 1.235 | |
getAnnotation | 1.702 | 0.083 | 68.927 | |
getDefaults | 0.001 | 0.000 | 0.000 | |
getInstalledAnnotations | 0.001 | 0.000 | 0.002 | |
getWeights | 0.001 | 0.000 | 0.001 | |
importCustomAnnotation | 0.944 | 0.006 | 0.950 | |
loadAnnotation | 0.001 | 0.000 | 0.002 | |
makeSimDataSd | 1.201 | 0.016 | 1.221 | |
makeSimDataTcc | 3.700 | 0.071 | 33.478 | |
metaTest | 0.009 | 0.006 | 0.015 | |
metaseqr2 | 5.697 | 0.623 | 315.538 | |
metaseqrPlot | 1.358 | 0.063 | 1.437 | |
normalizeAbsseq | 1.429 | 0.096 | 1.533 | |
normalizeDeseq | 0.369 | 0.035 | 0.405 | |
normalizeDeseq2 | 1.179 | 0.039 | 1.221 | |
normalizeDss | 0.534 | 0.040 | 0.575 | |
normalizeEdaseq | 0.638 | 0.030 | 0.675 | |
normalizeEdger | 0.281 | 0.030 | 0.313 | |
normalizeNbpseq | 0.266 | 0.035 | 0.303 | |
normalizeNoiseq | 0.345 | 0.035 | 0.386 | |
read2count | 13.244 | 1.753 | 17.891 | |
readTargets | 0.037 | 0.007 | 0.044 | |
statAbsseq | 3.436 | 0.109 | 3.779 | |
statDeseq | 1.674 | 0.030 | 1.713 | |
statDeseq2 | 7.315 | 0.106 | 7.583 | |
statDss | 1.743 | 0.030 | 1.824 | |
statEdger | 1.009 | 0.022 | 1.035 | |
statLimma | 0.792 | 0.006 | 0.801 | |
statNbpseq | 1.811 | 0.030 | 1.849 | |
statNoiseq | 16.460 | 0.092 | 17.161 | |