Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings metaseqR2_1.18.0.tar.gz |
StartedAt: 2024-12-20 02:24:44 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 02:42:48 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1083.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metaseqR2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings metaseqR2_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/metaseqR2.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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: ‘gcc (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 ... 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 read2count 8.911 1.213 13.371 statNoiseq 6.351 0.334 6.685 metaseqr2 5.084 0.777 10.109 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/metaseqR2.Rcheck/00check.log’ for details.
metaseqR2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL metaseqR2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘metaseqR2’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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 -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o metaseqR2.so pval.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-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-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. > 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 2024-12-20 02:35:41: 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: /home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp3u3aKo 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 /home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp3u3aKo/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 02:35:41: Data processing finished! Total processing time: 00 seconds Estimating AUFC weights... Please wait... Processing edger Processing limma Retrieving edger Retrieving limma 2024-12-20 02:35:42: 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: /home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp3u3aKo 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 /home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp3u3aKo/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 /home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp3u3aKo/data/reportdb.js Creating HTML report... Compressing figures... adding: home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp3u3aKo/plots/qc/mds.png (deflated 44%) 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/bin/pandoc +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp3u3aKo/index.html --lua-filter /home/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.20-bioc/R/site-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 /home/biocbuild/bbs-3.20-bioc/R/site-library/rmdformats/templates/material/material.html --highlight-style kate --variable theme=bootstrap --include-in-header /home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp3u3aKo/rmarkdown-str38893518486305.html Output created: /home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp3u3aKo/index.html 2024-12-20 02:35:50: Data processing finished! Total processing time: 08 seconds RUNIT TEST PROTOCOL -- Fri Dec 20 02:35:50 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 25.597 1.621 32.369
metaseqR2.Rcheck/metaseqR2-Ex.timings
name | user | system | elapsed | |
buildAnnotationDatabase | 0 | 0 | 0 | |
buildCustomAnnotation | 3.753 | 0.096 | 3.849 | |
combineBonferroni | 0 | 0 | 0 | |
combineHarmonic | 0.001 | 0.000 | 0.001 | |
combineMaxp | 0 | 0 | 0 | |
combineMinp | 0 | 0 | 0 | |
combineSimes | 0.000 | 0.000 | 0.001 | |
combineWeight | 0.000 | 0.000 | 0.001 | |
createSignalTracks | 0.906 | 0.057 | 0.959 | |
diagplotAvgFtd | 0.042 | 0.000 | 0.042 | |
diagplotBoxplot | 0.522 | 0.004 | 0.526 | |
diagplotCor | 0.100 | 0.003 | 0.103 | |
diagplotDeHeatmap | 0.655 | 0.003 | 0.658 | |
diagplotEdaseq | 0.340 | 0.005 | 0.345 | |
diagplotFiltered | 0.019 | 0.003 | 0.022 | |
diagplotFtd | 0.015 | 0.000 | 0.015 | |
diagplotMds | 0.167 | 0.001 | 0.169 | |
diagplotNoiseq | 0.354 | 0.006 | 0.360 | |
diagplotPairs | 0.715 | 0.007 | 0.722 | |
diagplotRoc | 0.015 | 0.001 | 0.017 | |
diagplotVenn | 0.155 | 0.014 | 0.170 | |
diagplotVolcano | 2.162 | 0.048 | 2.211 | |
downsampleCounts | 0.157 | 0.000 | 0.158 | |
estimateAufcWeights | 0.937 | 0.047 | 0.973 | |
estimateSimParams | 0.672 | 0.057 | 0.727 | |
getAnnotation | 1.718 | 0.148 | 4.951 | |
getDefaults | 0.000 | 0.000 | 0.001 | |
getInstalledAnnotations | 0.001 | 0.000 | 0.001 | |
getWeights | 0 | 0 | 0 | |
importCustomAnnotation | 0.760 | 0.067 | 0.828 | |
loadAnnotation | 0.001 | 0.001 | 0.001 | |
makeSimDataSd | 0.728 | 0.161 | 0.885 | |
makeSimDataTcc | 0.001 | 0.000 | 0.001 | |
metaTest | 0.005 | 0.006 | 0.009 | |
metaseqr2 | 5.084 | 0.777 | 10.109 | |
metaseqrPlot | 0.478 | 0.005 | 0.483 | |
normalizeAbsseq | 0.581 | 0.043 | 0.624 | |
normalizeDeseq | 0.124 | 0.003 | 0.127 | |
normalizeDeseq2 | 0.449 | 0.009 | 0.457 | |
normalizeDss | 0.192 | 0.004 | 0.196 | |
normalizeEdaseq | 0.342 | 0.012 | 0.354 | |
normalizeEdger | 0.090 | 0.009 | 0.099 | |
normalizeNbpseq | 0.083 | 0.005 | 0.088 | |
normalizeNoiseq | 0.124 | 0.005 | 0.129 | |
read2count | 8.911 | 1.213 | 13.371 | |
readTargets | 0.02 | 0.00 | 0.02 | |
statAbsseq | 1.166 | 0.063 | 1.229 | |
statDeseq | 0.765 | 0.009 | 0.774 | |
statDeseq2 | 3.055 | 0.193 | 3.248 | |
statDss | 0.622 | 0.016 | 0.639 | |
statEdger | 0.457 | 0.016 | 0.473 | |
statLimma | 0.239 | 0.002 | 0.242 | |
statNbpseq | 0.783 | 0.006 | 0.790 | |
statNoiseq | 6.351 | 0.334 | 6.685 | |