Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-13 12:03 -0400 (Mon, 13 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 1463/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
notame 0.99.6 (landing page) Vilhelm Suksi
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | NA | NA | NA | ||||||||||
To the developers/maintainers of the notame package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/notame.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: notame |
Version: 0.99.6 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:notame.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings notame_0.99.6.tar.gz |
StartedAt: 2025-10-13 02:24:13 -0400 (Mon, 13 Oct 2025) |
EndedAt: 2025-10-13 02:31:17 -0400 (Mon, 13 Oct 2025) |
EllapsedTime: 424.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: notame.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:notame.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings notame_0.99.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/notame.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘notame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘notame’ version ‘0.99.6’ * 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 ‘notame’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 whether startup messages can be suppressed ... 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 pca_bhattacharyya_dist 6.390 0.631 7.022 impute_rf 5.257 0.196 5.455 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/notame.Rcheck/00check.log’ for details.
notame.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL notame ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘notame’ ... ** this is package ‘notame’ version ‘0.99.6’ ** 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 (notame)
notame.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 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. > library(testthat) > library(notame) Loading required package: ggplot2 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: Seqinfo 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("notame") Running tests in parallel requires the 3rd edition INFO [2025-10-13 02:27:54] Pheno data was cleaned INFO [2025-10-13 02:27:54] Checking provided sample ID column INFO [2025-10-13 02:27:54] Column 'Sample_ID' created from id INFO [2025-10-13 02:27:54] Pheno data was cleaned INFO [2025-10-13 02:27:54] Sample ID generated from injection orders and prefix ID_ INFO [2025-10-13 02:27:54] Pheno data was cleaned INFO [2025-10-13 02:27:54] Pheno data was cleaned INFO [2025-10-13 02:27:54] Adding running index to 'QC' sample IDs INFO [2025-10-13 02:27:54] Pheno data was cleaned INFO [2025-10-13 02:27:54] Initializing 'Flag' column with unflagged features INFO [2025-10-13 02:27:54] Assigning HILIC_pos as the value of the Split column for each feature INFO [2025-10-13 02:27:54] Feature data was cleaned INFO [2025-10-13 02:27:54] Initializing 'Flag' column with unflagged features INFO [2025-10-13 02:27:54] Feature_ID column not found, creating feature IDs INFO [2025-10-13 02:27:54] Initializing 'Flag' column with unflagged features INFO [2025-10-13 02:27:54] Feature_ID column not found, creating feature IDs INFO [2025-10-13 02:27:54] Initializing 'Flag' column with unflagged features INFO [2025-10-13 02:27:54] Feature_ID column not found, creating feature IDs INFO [2025-10-13 02:27:54] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-13 02:27:54] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-13 02:27:54] Creating feature IDs from Split, m/z and retention time INFO [2025-10-13 02:27:54] Feature data was cleaned INFO [2025-10-13 02:27:54] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:54] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:54] Creating feature IDs from Split, m/z and retention time INFO [2025-10-13 02:27:55] Corner detected correctly at row 4, column D INFO [2025-10-13 02:27:55] Extracting sample information from rows 1 to 4 and columns E to P INFO [2025-10-13 02:27:55] Replacing spaces in sample information column names with underscores (_) INFO [2025-10-13 02:27:55] Naming the last column of sample information "easy_Datafile" INFO [2025-10-13 02:27:55] Extracting feature information from rows 5 to 14 and columns A to D INFO [2025-10-13 02:27:55] Extracting feature abundances from rows 5 to 14 and columns E to P INFO [2025-10-13 02:27:55] Sample ID generated from injection orders and prefix TEST_ INFO [2025-10-13 02:27:55] Pheno data was cleaned INFO [2025-10-13 02:27:55] Initializing 'Flag' column with unflagged features INFO [2025-10-13 02:27:55] Assigning easy as the value of the Split column for each feature INFO [2025-10-13 02:27:55] Feature_ID column not found, creating feature IDs INFO [2025-10-13 02:27:55] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:55] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:55] Creating feature IDs from Split, m/z and retention time INFO [2025-10-13 02:27:55] Feature data was cleaned INFO [2025-10-13 02:27:55] Checking sample information INFO [2025-10-13 02:27:55] Checking 'Injection_order' column in feature data INFO [2025-10-13 02:27:55] Checking 'Sample_ID' column in pheno data INFO [2025-10-13 02:27:55] Checking 'QC' column in feature data INFO [2025-10-13 02:27:55] Checking that feature abundances only contain numeric values INFO [2025-10-13 02:27:55] Checking feature information INFO [2025-10-13 02:27:55] Checking that feature IDs are unique and not storedas numbers INFO [2025-10-13 02:27:55] Checking that m/z and retention time values are reasonable. INFO [2025-10-13 02:27:55] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:55] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:55] Checking that feature data includes a 'Split' column INFO [2025-10-13 02:27:55] Checking that feature data includes a 'Flag' column INFO [2025-10-13 02:27:55] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:55] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:55] Creating feature IDs from Split, m/z and retention time INFO [2025-10-13 02:27:55] Corner detected correctly at row 4, column F INFO [2025-10-13 02:27:55] Extracting sample information from rows 1 to 4 and columns G to R INFO [2025-10-13 02:27:55] Replacing spaces in sample information column names with underscores (_) INFO [2025-10-13 02:27:55] Naming the last column of sample information "Datafile" INFO [2025-10-13 02:27:55] Extracting feature information from rows 5 to 20 and columns A to F INFO [2025-10-13 02:27:55] Extracting feature abundances from rows 5 to 20 and columns G to R INFO [2025-10-13 02:27:55] Sample ID generated from injection orders and prefix TEST_ INFO [2025-10-13 02:27:55] Pheno data was cleaned INFO [2025-10-13 02:27:55] Initializing 'Flag' column with unflagged features INFO [2025-10-13 02:27:55] Creating Split column from Column, Mode INFO [2025-10-13 02:27:55] Feature_ID column not found, creating feature IDs INFO [2025-10-13 02:27:55] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:55] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:55] Creating feature IDs from Split, m/z and retention time INFO [2025-10-13 02:27:55] Feature data was cleaned INFO [2025-10-13 02:27:55] Checking sample information INFO [2025-10-13 02:27:55] Checking 'Injection_order' column in feature data INFO [2025-10-13 02:27:55] Checking 'Sample_ID' column in pheno data INFO [2025-10-13 02:27:55] Checking 'QC' column in feature data INFO [2025-10-13 02:27:55] Checking that feature abundances only contain numeric values INFO [2025-10-13 02:27:55] Checking feature information INFO [2025-10-13 02:27:55] Checking that feature IDs are unique and not storedas numbers INFO [2025-10-13 02:27:55] Checking that m/z and retention time values are reasonable. INFO [2025-10-13 02:27:55] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:55] Identified m/z column Mass and retention time column RetentionTime INFO [2025-10-13 02:27:55] Checking that feature data includes a 'Split' column INFO [2025-10-13 02:27:55] Checking that feature data includes a 'Flag' column INFO [2025-10-13 02:27:55] Pheno data was cleaned INFO [2025-10-13 02:27:55] Feature data was cleaned INFO [2025-10-13 02:27:55] Pheno data was cleaned INFO [2025-10-13 02:27:55] Feature data was cleaned INFO [2025-10-13 02:27:55] Detecting corner position INFO [2025-10-13 02:27:55] Corner detected correctly at row 11, column H INFO [2025-10-13 02:27:55] Extracting sample information from rows 1 to 11 and columns I to BF INFO [2025-10-13 02:27:55] Replacing spaces in sample information column names with underscores (_) INFO [2025-10-13 02:27:55] Naming the last column of sample information "hilic_neg_Datafile" INFO [2025-10-13 02:27:55] Extracting feature information from rows 12 to 31 and columns A to H INFO [2025-10-13 02:27:55] Extracting feature abundances from rows 12 to 31 and columns I to BF INFO [2025-10-13 02:27:55] Pheno data was cleaned INFO [2025-10-13 02:27:56] Feature data was cleaned INFO [2025-10-13 02:27:56] Checking sample information INFO [2025-10-13 02:27:56] Checking 'Injection_order' column in feature data INFO [2025-10-13 02:27:56] Checking 'Sample_ID' column in pheno data INFO [2025-10-13 02:27:56] Checking 'QC' column in feature data INFO [2025-10-13 02:27:56] Checking that feature abundances only contain numeric values INFO [2025-10-13 02:27:56] Checking feature information INFO [2025-10-13 02:27:56] Checking that feature IDs are unique and not storedas numbers INFO [2025-10-13 02:27:56] Checking that m/z and retention time values are reasonable. INFO [2025-10-13 02:27:56] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-13 02:27:56] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-13 02:27:56] Checking that feature data includes a 'Split' column INFO [2025-10-13 02:27:56] Checking that feature data includes a 'Flag' column INFO [2025-10-13 02:27:56] Detecting corner position INFO [2025-10-13 02:27:56] Corner detected correctly at row 11, column H INFO [2025-10-13 02:27:56] Extracting sample information from rows 1 to 11 and columns I to BF INFO [2025-10-13 02:27:56] Replacing spaces in sample information column names with underscores (_) INFO [2025-10-13 02:27:56] Naming the last column of sample information "hilic_pos_Datafile" INFO [2025-10-13 02:27:56] Extracting feature information from rows 12 to 31 and columns A to H INFO [2025-10-13 02:27:56] Extracting feature abundances from rows 12 to 31 and columns I to BF INFO [2025-10-13 02:27:56] Pheno data was cleaned INFO [2025-10-13 02:27:56] Feature data was cleaned INFO [2025-10-13 02:27:56] Checking sample information INFO [2025-10-13 02:27:56] Checking 'Injection_order' column in feature data INFO [2025-10-13 02:27:56] Checking 'Sample_ID' column in pheno data INFO [2025-10-13 02:27:56] Checking 'QC' column in feature data INFO [2025-10-13 02:27:56] Checking that feature abundances only contain numeric values INFO [2025-10-13 02:27:56] Checking feature information INFO [2025-10-13 02:27:56] Checking that feature IDs are unique and not storedas numbers INFO [2025-10-13 02:27:56] Checking that m/z and retention time values are reasonable. INFO [2025-10-13 02:27:56] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-13 02:27:56] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-13 02:27:56] Checking that feature data includes a 'Split' column INFO [2025-10-13 02:27:56] Checking that feature data includes a 'Flag' column INFO [2025-10-13 02:27:56] Detecting corner position INFO [2025-10-13 02:27:56] Corner detected correctly at row 11, column H INFO [2025-10-13 02:27:56] Extracting sample information from rows 1 to 11 and columns I to BF INFO [2025-10-13 02:27:56] Replacing spaces in sample information column names with underscores (_) INFO [2025-10-13 02:27:56] Naming the last column of sample information "rp_neg_Datafile" INFO [2025-10-13 02:27:56] Extracting feature information from rows 12 to 31 and columns A to H INFO [2025-10-13 02:27:56] Extracting feature abundances from rows 12 to 31 and columns I to BF INFO [2025-10-13 02:27:56] Pheno data was cleaned INFO [2025-10-13 02:27:56] Feature data was cleaned INFO [2025-10-13 02:27:56] Checking sample information INFO [2025-10-13 02:27:56] Checking 'Injection_order' column in feature data INFO [2025-10-13 02:27:56] Checking 'Sample_ID' column in pheno data INFO [2025-10-13 02:27:56] Checking 'QC' column in feature data INFO [2025-10-13 02:27:56] Checking that feature abundances only contain numeric values INFO [2025-10-13 02:27:56] Checking feature information INFO [2025-10-13 02:27:56] Checking that feature IDs are unique and not storedas numbers INFO [2025-10-13 02:27:56] Checking that m/z and retention time values are reasonable. INFO [2025-10-13 02:27:56] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-13 02:27:56] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-13 02:27:56] Checking that feature data includes a 'Split' column INFO [2025-10-13 02:27:56] Checking that feature data includes a 'Flag' column INFO [2025-10-13 02:27:56] Detecting corner position INFO [2025-10-13 02:27:56] Corner detected correctly at row 11, column H INFO [2025-10-13 02:27:56] Extracting sample information from rows 1 to 11 and columns I to BF INFO [2025-10-13 02:27:56] Replacing spaces in sample information column names with underscores (_) INFO [2025-10-13 02:27:56] Naming the last column of sample information "rp_pos_Datafile" INFO [2025-10-13 02:27:56] Extracting feature information from rows 12 to 31 and columns A to H INFO [2025-10-13 02:27:56] Extracting feature abundances from rows 12 to 31 and columns I to BF INFO [2025-10-13 02:27:56] Pheno data was cleaned INFO [2025-10-13 02:27:56] Feature data was cleaned INFO [2025-10-13 02:27:56] Checking sample information INFO [2025-10-13 02:27:56] Checking 'Injection_order' column in feature data INFO [2025-10-13 02:27:56] Checking 'Sample_ID' column in pheno data INFO [2025-10-13 02:27:56] Checking 'QC' column in feature data INFO [2025-10-13 02:27:56] Checking that feature abundances only contain numeric values INFO [2025-10-13 02:27:56] Checking feature information INFO [2025-10-13 02:27:56] Checking that feature IDs are unique and not storedas numbers INFO [2025-10-13 02:27:56] Checking that m/z and retention time values are reasonable. INFO [2025-10-13 02:27:56] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-13 02:27:56] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-13 02:27:56] Checking that feature data includes a 'Split' column INFO [2025-10-13 02:27:56] Checking that feature data includes a 'Flag' column INFO [2025-10-13 02:27:56] Injection order differs between modes.Creating dummy injection order INFO [2025-10-13 02:27:56] Dummy injection order (row numbers) created INFO [2025-10-13 02:27:56] Merging objects with unequal amounts of samples. INFO [2025-10-13 02:27:56] Samples only in first object: INFO [2025-10-13 02:27:56] ID_666 INFO [2025-10-13 02:27:56] Samples only in second object: INFO [2025-10-13 02:27:56] Demo_2 INFO [2025-10-13 02:27:56] Injection order differs between modes.Creating dummy injection order INFO [2025-10-13 02:27:56] Dummy injection order (row numbers) created INFO [2025-10-13 02:27:57] Merging objects with unequal amounts of samples. INFO [2025-10-13 02:27:57] Samples only in first object: INFO [2025-10-13 02:27:57] ID_666 INFO [2025-10-13 02:27:57] Samples only in second object: INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] Injection order differs between modes.Creating dummy injection order INFO [2025-10-13 02:27:57] Dummy injection order (row numbers) created INFO [2025-10-13 02:27:57] Merging objects with unequal amounts of samples. INFO [2025-10-13 02:27:57] Samples only in first object: INFO [2025-10-13 02:27:57] ID_666, Demo_22 INFO [2025-10-13 02:27:57] Samples only in second object: INFO [2025-10-13 02:27:57] ID_999 INFO [2025-10-13 02:27:57] Starting logging INFO [2025-10-13 02:27:57] Finished analysis. Mon Oct 13 02:27:57 2025 Session info: INFO [2025-10-13 02:27:57] R version 4.5.1 Patched (2025-08-23 r88802) INFO [2025-10-13 02:27:57] Platform: x86_64-pc-linux-gnu INFO [2025-10-13 02:27:57] Running under: Ubuntu 24.04.3 LTS INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] Matrix products: default INFO [2025-10-13 02:27:57] BLAS: /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so INFO [2025-10-13 02:27:57] LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0 INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] locale: INFO [2025-10-13 02:27:57] [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C INFO [2025-10-13 02:27:57] [3] LC_TIME=en_GB LC_COLLATE=C INFO [2025-10-13 02:27:57] [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 INFO [2025-10-13 02:27:57] [7] LC_PAPER=en_US.UTF-8 LC_NAME=C INFO [2025-10-13 02:27:57] [9] LC_ADDRESS=C LC_TELEPHONE=C INFO [2025-10-13 02:27:57] [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] time zone: America/New_York INFO [2025-10-13 02:27:57] tzcode source: system (glibc) INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] attached base packages: INFO [2025-10-13 02:27:57] [1] stats4 stats graphics grDevices utils datasets methods INFO [2025-10-13 02:27:57] [8] base INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] other attached packages: INFO [2025-10-13 02:27:57] [1] notame_0.99.6 SummarizedExperiment_1.39.2 INFO [2025-10-13 02:27:57] [3] Biobase_2.69.1 GenomicRanges_1.61.5 INFO [2025-10-13 02:27:57] [5] Seqinfo_0.99.2 IRanges_2.43.5 INFO [2025-10-13 02:27:57] [7] S4Vectors_0.47.4 BiocGenerics_0.55.3 INFO [2025-10-13 02:27:57] [9] generics_0.1.4 MatrixGenerics_1.21.0 INFO [2025-10-13 02:27:57] [11] matrixStats_1.5.0 ggplot2_4.0.0 INFO [2025-10-13 02:27:57] [13] testthat_3.2.3 INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] loaded via a namespace (and not attached): INFO [2025-10-13 02:27:57] [1] Matrix_1.7-4 gtable_0.3.6 futile.logger_1.4.3 INFO [2025-10-13 02:27:57] [4] dplyr_1.1.4 compiler_4.5.1 crayon_1.5.3 INFO [2025-10-13 02:27:57] [7] brio_1.1.5 zip_2.3.3 Rcpp_1.1.0 INFO [2025-10-13 02:27:57] [10] tidyselect_1.2.1 tidyr_1.3.1 scales_1.4.0 INFO [2025-10-13 02:27:57] [13] lattice_0.22-7 R6_2.6.1 XVector_0.49.1 INFO [2025-10-13 02:27:57] [16] S4Arrays_1.9.1 openxlsx_4.2.8 DelayedArray_0.35.3 INFO [2025-10-13 02:27:57] [19] tibble_3.3.0 desc_1.4.3 pillar_1.11.1 INFO [2025-10-13 02:27:57] [22] RColorBrewer_1.1-3 rlang_1.1.6 stringi_1.8.7 INFO [2025-10-13 02:27:57] [25] S7_0.2.0 viridisLite_0.4.2 SparseArray_1.9.1 INFO [2025-10-13 02:27:57] [28] cli_3.6.5 formatR_1.14 withr_3.0.2 INFO [2025-10-13 02:27:57] [31] magrittr_2.0.4 futile.options_1.0.1 grid_4.5.1 INFO [2025-10-13 02:27:57] [34] lifecycle_1.0.4 waldo_0.6.2 vctrs_0.6.5 INFO [2025-10-13 02:27:57] [37] glue_1.8.0 lambda.r_1.2.4 farver_2.1.2 INFO [2025-10-13 02:27:57] [40] abind_1.4-8 purrr_1.1.0 tools_4.5.1 INFO [2025-10-13 02:27:57] [43] pkgconfig_2.0.3 INFO [2025-10-13 02:27:57] New line INFO [2025-10-13 02:27:57] Starting logging INFO [2025-10-13 02:27:57] New line INFO [2025-10-13 02:27:57] Finished analysis. Mon Oct 13 02:27:57 2025 Session info: INFO [2025-10-13 02:27:57] R version 4.5.1 Patched (2025-08-23 r88802) INFO [2025-10-13 02:27:57] Platform: x86_64-pc-linux-gnu INFO [2025-10-13 02:27:57] Running under: Ubuntu 24.04.3 LTS INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] Matrix products: default INFO [2025-10-13 02:27:57] BLAS: /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so INFO [2025-10-13 02:27:57] LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0 INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] locale: INFO [2025-10-13 02:27:57] [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C INFO [2025-10-13 02:27:57] [3] LC_TIME=en_GB LC_COLLATE=C INFO [2025-10-13 02:27:57] [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 INFO [2025-10-13 02:27:57] [7] LC_PAPER=en_US.UTF-8 LC_NAME=C INFO [2025-10-13 02:27:57] [9] LC_ADDRESS=C LC_TELEPHONE=C INFO [2025-10-13 02:27:57] [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] time zone: America/New_York INFO [2025-10-13 02:27:57] tzcode source: system (glibc) INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] attached base packages: INFO [2025-10-13 02:27:57] [1] stats4 stats graphics grDevices utils datasets methods INFO [2025-10-13 02:27:57] [8] base INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] other attached packages: INFO [2025-10-13 02:27:57] [1] notame_0.99.6 SummarizedExperiment_1.39.2 INFO [2025-10-13 02:27:57] [3] Biobase_2.69.1 GenomicRanges_1.61.5 INFO [2025-10-13 02:27:57] [5] Seqinfo_0.99.2 IRanges_2.43.5 INFO [2025-10-13 02:27:57] [7] S4Vectors_0.47.4 BiocGenerics_0.55.3 INFO [2025-10-13 02:27:57] [9] generics_0.1.4 MatrixGenerics_1.21.0 INFO [2025-10-13 02:27:57] [11] matrixStats_1.5.0 ggplot2_4.0.0 INFO [2025-10-13 02:27:57] [13] testthat_3.2.3 INFO [2025-10-13 02:27:57] INFO [2025-10-13 02:27:57] loaded via a namespace (and not attached): INFO [2025-10-13 02:27:57] [1] Matrix_1.7-4 gtable_0.3.6 futile.logger_1.4.3 INFO [2025-10-13 02:27:57] [4] dplyr_1.1.4 compiler_4.5.1 crayon_1.5.3 INFO [2025-10-13 02:27:57] [7] brio_1.1.5 zip_2.3.3 Rcpp_1.1.0 INFO [2025-10-13 02:27:57] [10] tidyselect_1.2.1 tidyr_1.3.1 scales_1.4.0 INFO [2025-10-13 02:27:57] [13] lattice_0.22-7 R6_2.6.1 XVector_0.49.1 INFO [2025-10-13 02:27:57] [16] S4Arrays_1.9.1 openxlsx_4.2.8 DelayedArray_0.35.3 INFO [2025-10-13 02:27:57] [19] tibble_3.3.0 desc_1.4.3 pillar_1.11.1 INFO [2025-10-13 02:27:57] [22] RColorBrewer_1.1-3 rlang_1.1.6 stringi_1.8.7 INFO [2025-10-13 02:27:57] [25] S7_0.2.0 viridisLite_0.4.2 SparseArray_1.9.1 INFO [2025-10-13 02:27:57] [28] cli_3.6.5 formatR_1.14 withr_3.0.2 INFO [2025-10-13 02:27:57] [31] magrittr_2.0.4 futile.options_1.0.1 grid_4.5.1 INFO [2025-10-13 02:27:57] [34] lifecycle_1.0.4 waldo_0.6.2 vctrs_0.6.5 INFO [2025-10-13 02:27:57] [37] glue_1.8.0 lambda.r_1.2.4 farver_2.1.2 INFO [2025-10-13 02:27:57] [40] abind_1.4-8 purrr_1.1.0 tools_4.5.1 INFO [2025-10-13 02:27:57] [43] pkgconfig_2.0.3 INFO [2025-10-13 02:27:57] New line INFO [2025-10-13 02:27:57] Starting random forest imputation at 2025-10-13 02:27:57.697978 INFO [2025-10-13 02:28:03] Out-of-bag error in random forest imputation: 0.469 INFO [2025-10-13 02:28:03] Random forest imputation finished at 2025-10-13 02:28:03.924252 INFO [2025-10-13 02:28:04] Starting random forest imputation at 2025-10-13 02:28:04.186865 INFO [2025-10-13 02:28:07] Out-of-bag error in random forest imputation: 0.47 INFO [2025-10-13 02:28:07] Random forest imputation finished at 2025-10-13 02:28:07.978449 INFO [2025-10-13 02:28:07] Starting random forest imputation at 2025-10-13 02:28:07.995181 INFO [2025-10-13 02:28:11] Out-of-bag error in random forest imputation: 0.47 INFO [2025-10-13 02:28:11] Random forest imputation finished at 2025-10-13 02:28:11.861576 INFO [2025-10-13 02:28:11] Starting random forest imputation at 2025-10-13 02:28:11.902139 INFO [2025-10-13 02:28:16] Out-of-bag error in random forest imputation: 0.467 INFO [2025-10-13 02:28:17] Random forest imputation finished at 2025-10-13 02:28:17.026409 INFO [2025-10-13 02:28:17] Starting PQN normalization INFO [2025-10-13 02:28:17] Using median of qc samples as reference spectrum INFO [2025-10-13 02:28:17] Starting PQN normalization INFO [2025-10-13 02:28:17] Using median of all samples as reference spectrum INFO [2025-10-13 02:28:17] Starting PQN normalization INFO [2025-10-13 02:28:17] Using mean of qc samples as reference spectrum INFO [2025-10-13 02:28:17] Starting PQN normalization INFO [2025-10-13 02:28:17] Using mean of all samples as reference spectrum INFO [2025-10-13 02:28:20] 92% of features flagged for low quality INFO [2025-10-13 02:28:20] Starting PQN normalization INFO [2025-10-13 02:28:20] Using median of qc samples as reference spectrum INFO [2025-10-13 02:28:20] Starting drift correction at 2025-10-13 02:28:20.895446 INFO [2025-10-13 02:28:20] Zero values in feature abundances detected. Zeroes will be replaced with 1.1. INFO [2025-10-13 02:28:21] Drift correction performed at 2025-10-13 02:28:21.276921 INFO [2025-10-13 02:28:21] Inspecting drift correction results 2025-10-13 02:28:21.488888 INFO [2025-10-13 02:28:21] Drift correction results inspected at 2025-10-13 02:28:21.915137 INFO [2025-10-13 02:28:21] Drift correction results inspected, report: Drift_corrected: 100% [ FAIL 0 | WARN 5 | SKIP 0 | PASS 84 ] [ FAIL 0 | WARN 5 | SKIP 0 | PASS 84 ] > > proc.time() user system elapsed 35.252 3.240 37.000
notame.Rcheck/notame-Ex.timings
name | user | system | elapsed | |
assess_quality | 2.937 | 0.326 | 2.986 | |
citations | 0.459 | 0.290 | 0.469 | |
cluster_features | 0.676 | 1.005 | 0.802 | |
combined_data | 0.053 | 0.005 | 0.058 | |
compress_clusters | 0.623 | 0.999 | 0.654 | |
correct_drift | 0.721 | 0.858 | 0.913 | |
drop_flagged | 0.281 | 0.329 | 0.297 | |
drop_qcs | 0.033 | 0.004 | 0.036 | |
finish_log | 0.025 | 0.013 | 0.042 | |
fix_MSMS | 0.100 | 0.005 | 0.104 | |
fix_object | 0.122 | 0.022 | 0.144 | |
flag | 0.028 | 0.004 | 0.032 | |
flag_contaminants | 0.155 | 0.062 | 0.217 | |
flag_detection | 0.237 | 0.065 | 0.302 | |
flag_quality | 0.536 | 0.581 | 0.524 | |
flag_report | 0.498 | 0.367 | 0.530 | |
import_from_excel | 0.289 | 0.077 | 0.369 | |
impute_rf | 5.257 | 0.196 | 5.455 | |
impute_simple | 0.082 | 0.006 | 0.088 | |
init_log | 0.003 | 0.000 | 0.003 | |
inverse_normalize | 0.039 | 0.012 | 0.050 | |
join_colData | 0.034 | 0.003 | 0.036 | |
join_rowData | 0.023 | 0.003 | 0.026 | |
log_text | 0.003 | 0.002 | 0.005 | |
mark_nas | 0.040 | 0.002 | 0.042 | |
merge_notame_sets | 0.493 | 0.055 | 0.549 | |
pca_bhattacharyya_dist | 6.390 | 0.631 | 7.022 | |
perform_repeatability | 0.927 | 0.984 | 0.757 | |
pqn_normalization | 0.176 | 0.091 | 0.082 | |
quality | 0.264 | 0.421 | 0.305 | |
ruvs_qc | 0.170 | 0.021 | 0.191 | |
write_to_excel | 0.185 | 0.025 | 0.210 | |