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This page was generated on 2026-04-20 11:37 -0400 (Mon, 20 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 alpha (2026-04-05 r89794) 4961
kjohnson3macOS 13.7.7 Venturaarm644.6.0 alpha (2026-04-08 r89818) 4690
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4627
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 1497/2404HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
notame 1.1.4  (landing page)
Vilhelm Suksi
Snapshot Date: 2026-04-19 13:40 -0400 (Sun, 19 Apr 2026)
git_url: https://git.bioconductor.org/packages/notame
git_branch: devel
git_last_commit: ceb2b0f
git_last_commit_date: 2026-02-26 05:35:52 -0400 (Thu, 26 Feb 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  
See other builds for notame in R Universe.

CHECK results for notame on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: notame
Version: 1.1.4
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:notame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings notame_1.1.4.tar.gz
StartedAt: 2026-04-17 05:11:46 -0000 (Fri, 17 Apr 2026)
EndedAt: 2026-04-17 05:17:00 -0000 (Fri, 17 Apr 2026)
EllapsedTime: 314.2 seconds
RetCode: 0
Status:   OK  
CheckDir: notame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:notame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings notame_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/notame.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘notame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘notame’ version ‘1.1.4’
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/notame.Rcheck/00check.log’
for details.

Installation output

notame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL notame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘notame’ ...
** this is package ‘notame’ version ‘1.1.4’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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)

Tests output

notame.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 [2026-04-17 05:16:19] Pheno data was cleaned
INFO [2026-04-17 05:16:19] Checking provided sample ID column
INFO [2026-04-17 05:16:19] Column 'Sample_ID' created from id
INFO [2026-04-17 05:16:19] Pheno data was cleaned
INFO [2026-04-17 05:16:19] Sample ID generated from injection orders and prefix ID_
INFO [2026-04-17 05:16:19] Pheno data was cleaned
INFO [2026-04-17 05:16:19] Pheno data was cleaned
INFO [2026-04-17 05:16:19] Adding running index to 'QC' sample IDs
INFO [2026-04-17 05:16:19] Pheno data was cleaned
INFO [2026-04-17 05:16:19] Initializing 'Flag' column with unflagged features
INFO [2026-04-17 05:16:19] Assigning HILIC_pos as the value of the Split column for each feature
INFO [2026-04-17 05:16:19] Feature data was cleaned
INFO [2026-04-17 05:16:19] Initializing 'Flag' column with unflagged features
INFO [2026-04-17 05:16:19] Feature_ID column not found, creating feature IDs
INFO [2026-04-17 05:16:19] Initializing 'Flag' column with unflagged features
INFO [2026-04-17 05:16:19] Feature_ID column not found, creating feature IDs
INFO [2026-04-17 05:16:19] Initializing 'Flag' column with unflagged features
INFO [2026-04-17 05:16:19] Feature_ID column not found, creating feature IDs
INFO [2026-04-17 05:16:19] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:16:19] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:16:19] Creating feature IDs from Split, m/z and retention time
INFO [2026-04-17 05:16:19] Feature data was cleaned
INFO [2026-04-17 05:16:19] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:19] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:19] Creating feature IDs from Split, m/z and retention time
INFO [2026-04-17 05:16:19] Corner detected correctly at row 4, column D
INFO [2026-04-17 05:16:19] 
Extracting sample information from rows 1 to 4 and columns E to P
INFO [2026-04-17 05:16:19] Replacing spaces in sample information column names with underscores (_)
INFO [2026-04-17 05:16:19] Naming the last column of sample information "easy_Datafile"
INFO [2026-04-17 05:16:19] 
Extracting feature information from rows 5 to 14 and columns A to D
INFO [2026-04-17 05:16:19] 
Extracting feature abundances from rows 5 to 14 and columns E to P
INFO [2026-04-17 05:16:19] Sample ID generated from injection orders and prefix TEST_
INFO [2026-04-17 05:16:19] Pheno data was cleaned
INFO [2026-04-17 05:16:19] Initializing 'Flag' column with unflagged features
INFO [2026-04-17 05:16:19] Assigning easy as the value of the Split column for each feature
INFO [2026-04-17 05:16:19] Feature_ID column not found, creating feature IDs
INFO [2026-04-17 05:16:19] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:19] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:19] Creating feature IDs from Split, m/z and retention time
INFO [2026-04-17 05:16:19] Feature data was cleaned
INFO [2026-04-17 05:16:19] 
Checking sample information
INFO [2026-04-17 05:16:19] Checking 'Injection_order' column in feature data
INFO [2026-04-17 05:16:19] Checking 'Sample_ID' column in pheno data
INFO [2026-04-17 05:16:19] Checking 'QC' column in feature data
INFO [2026-04-17 05:16:19] Checking that feature abundances only contain numeric values
INFO [2026-04-17 05:16:19] 
Checking feature information
INFO [2026-04-17 05:16:19] Checking that feature IDs are unique and not storedas numbers
INFO [2026-04-17 05:16:19] Checking that m/z and retention time values are reasonable.
INFO [2026-04-17 05:16:19] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:19] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:19] Checking that feature data includes a 'Split' column
INFO [2026-04-17 05:16:19] Checking that feature data includes a 'Flag' column
INFO [2026-04-17 05:16:20] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:20] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:20] Creating feature IDs from Split, m/z and retention time
INFO [2026-04-17 05:16:20] Corner detected correctly at row 4, column F
INFO [2026-04-17 05:16:20] 
Extracting sample information from rows 1 to 4 and columns G to R
INFO [2026-04-17 05:16:20] Replacing spaces in sample information column names with underscores (_)
INFO [2026-04-17 05:16:20] Naming the last column of sample information "Datafile"
INFO [2026-04-17 05:16:20] 
Extracting feature information from rows 5 to 20 and columns A to F
INFO [2026-04-17 05:16:20] 
Extracting feature abundances from rows 5 to 20 and columns G to R
INFO [2026-04-17 05:16:20] Sample ID generated from injection orders and prefix TEST_
INFO [2026-04-17 05:16:20] Pheno data was cleaned
INFO [2026-04-17 05:16:20] Initializing 'Flag' column with unflagged features
INFO [2026-04-17 05:16:20] Creating Split column from Column, Mode
INFO [2026-04-17 05:16:20] Feature_ID column not found, creating feature IDs
INFO [2026-04-17 05:16:20] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:20] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:20] Creating feature IDs from Split, m/z and retention time
INFO [2026-04-17 05:16:20] Feature data was cleaned
INFO [2026-04-17 05:16:20] 
Checking sample information
INFO [2026-04-17 05:16:20] Checking 'Injection_order' column in feature data
INFO [2026-04-17 05:16:20] Checking 'Sample_ID' column in pheno data
INFO [2026-04-17 05:16:20] Checking 'QC' column in feature data
INFO [2026-04-17 05:16:20] Checking that feature abundances only contain numeric values
INFO [2026-04-17 05:16:20] 
Checking feature information
INFO [2026-04-17 05:16:20] Checking that feature IDs are unique and not storedas numbers
INFO [2026-04-17 05:16:20] Checking that m/z and retention time values are reasonable.
INFO [2026-04-17 05:16:20] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:20] Identified m/z column Mass and retention time column RetentionTime
INFO [2026-04-17 05:16:20] Checking that feature data includes a 'Split' column
INFO [2026-04-17 05:16:20] Checking that feature data includes a 'Flag' column
INFO [2026-04-17 05:16:20] Pheno data was cleaned
INFO [2026-04-17 05:16:20] Feature data was cleaned
INFO [2026-04-17 05:16:20] Pheno data was cleaned
INFO [2026-04-17 05:16:20] Feature data was cleaned
INFO [2026-04-17 05:16:20] Detecting corner position
INFO [2026-04-17 05:16:20] Corner detected correctly at row 11, column H
INFO [2026-04-17 05:16:20] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2026-04-17 05:16:20] Replacing spaces in sample information column names with underscores (_)
INFO [2026-04-17 05:16:20] Naming the last column of sample information "hilic_neg_Datafile"
INFO [2026-04-17 05:16:20] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2026-04-17 05:16:20] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2026-04-17 05:16:20] Pheno data was cleaned
INFO [2026-04-17 05:16:21] Feature data was cleaned
INFO [2026-04-17 05:16:21] 
Checking sample information
INFO [2026-04-17 05:16:21] Checking 'Injection_order' column in feature data
INFO [2026-04-17 05:16:21] Checking 'Sample_ID' column in pheno data
INFO [2026-04-17 05:16:21] Checking 'QC' column in feature data
INFO [2026-04-17 05:16:21] Checking that feature abundances only contain numeric values
INFO [2026-04-17 05:16:21] 
Checking feature information
INFO [2026-04-17 05:16:21] Checking that feature IDs are unique and not storedas numbers
INFO [2026-04-17 05:16:21] Checking that m/z and retention time values are reasonable.
INFO [2026-04-17 05:16:21] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:16:21] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:16:21] Checking that feature data includes a 'Split' column
INFO [2026-04-17 05:16:21] Checking that feature data includes a 'Flag' column
INFO [2026-04-17 05:16:21] Detecting corner position
INFO [2026-04-17 05:16:21] Corner detected correctly at row 11, column H
INFO [2026-04-17 05:16:21] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2026-04-17 05:16:21] Replacing spaces in sample information column names with underscores (_)
INFO [2026-04-17 05:16:21] Naming the last column of sample information "hilic_pos_Datafile"
INFO [2026-04-17 05:16:21] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2026-04-17 05:16:21] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2026-04-17 05:16:21] Pheno data was cleaned
INFO [2026-04-17 05:16:21] Feature data was cleaned
INFO [2026-04-17 05:16:21] 
Checking sample information
INFO [2026-04-17 05:16:21] Checking 'Injection_order' column in feature data
INFO [2026-04-17 05:16:21] Checking 'Sample_ID' column in pheno data
INFO [2026-04-17 05:16:21] Checking 'QC' column in feature data
INFO [2026-04-17 05:16:21] Checking that feature abundances only contain numeric values
INFO [2026-04-17 05:16:21] 
Checking feature information
INFO [2026-04-17 05:16:21] Checking that feature IDs are unique and not storedas numbers
INFO [2026-04-17 05:16:21] Checking that m/z and retention time values are reasonable.
INFO [2026-04-17 05:16:21] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:16:21] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:16:21] Checking that feature data includes a 'Split' column
INFO [2026-04-17 05:16:21] Checking that feature data includes a 'Flag' column
INFO [2026-04-17 05:16:21] Detecting corner position
INFO [2026-04-17 05:16:21] Corner detected correctly at row 11, column H
INFO [2026-04-17 05:16:21] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2026-04-17 05:16:21] Replacing spaces in sample information column names with underscores (_)
INFO [2026-04-17 05:16:21] Naming the last column of sample information "rp_neg_Datafile"
INFO [2026-04-17 05:16:21] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2026-04-17 05:16:21] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2026-04-17 05:16:21] Pheno data was cleaned
INFO [2026-04-17 05:16:21] Feature data was cleaned
INFO [2026-04-17 05:16:21] 
Checking sample information
INFO [2026-04-17 05:16:21] Checking 'Injection_order' column in feature data
INFO [2026-04-17 05:16:21] Checking 'Sample_ID' column in pheno data
INFO [2026-04-17 05:16:21] Checking 'QC' column in feature data
INFO [2026-04-17 05:16:21] Checking that feature abundances only contain numeric values
INFO [2026-04-17 05:16:21] 
Checking feature information
INFO [2026-04-17 05:16:21] Checking that feature IDs are unique and not storedas numbers
INFO [2026-04-17 05:16:21] Checking that m/z and retention time values are reasonable.
INFO [2026-04-17 05:16:21] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:16:21] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:16:21] Checking that feature data includes a 'Split' column
INFO [2026-04-17 05:16:21] Checking that feature data includes a 'Flag' column
INFO [2026-04-17 05:16:21] Detecting corner position
INFO [2026-04-17 05:16:21] Corner detected correctly at row 11, column H
INFO [2026-04-17 05:16:21] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2026-04-17 05:16:21] Replacing spaces in sample information column names with underscores (_)
INFO [2026-04-17 05:16:21] Naming the last column of sample information "rp_pos_Datafile"
INFO [2026-04-17 05:16:21] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2026-04-17 05:16:21] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2026-04-17 05:16:21] Pheno data was cleaned
INFO [2026-04-17 05:16:21] Feature data was cleaned
INFO [2026-04-17 05:16:21] 
Checking sample information
INFO [2026-04-17 05:16:21] Checking 'Injection_order' column in feature data
INFO [2026-04-17 05:16:21] Checking 'Sample_ID' column in pheno data
INFO [2026-04-17 05:16:21] Checking 'QC' column in feature data
INFO [2026-04-17 05:16:21] Checking that feature abundances only contain numeric values
INFO [2026-04-17 05:16:21] 
Checking feature information
INFO [2026-04-17 05:16:21] Checking that feature IDs are unique and not storedas numbers
INFO [2026-04-17 05:16:21] Checking that m/z and retention time values are reasonable.
INFO [2026-04-17 05:16:21] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:16:21] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:16:21] Checking that feature data includes a 'Split' column
INFO [2026-04-17 05:16:21] Checking that feature data includes a 'Flag' column
INFO [2026-04-17 05:16:21] Injection order differs between modes.Creating dummy injection order
INFO [2026-04-17 05:16:22] Dummy injection order (row numbers) created
INFO [2026-04-17 05:16:22] Merging objects with unequal amounts of samples.
INFO [2026-04-17 05:16:22] Samples only in first object:
INFO [2026-04-17 05:16:22] ID_666

INFO [2026-04-17 05:16:22] Samples only in second object:
INFO [2026-04-17 05:16:22] Demo_2

INFO [2026-04-17 05:16:22] Injection order differs between modes.Creating dummy injection order
INFO [2026-04-17 05:16:22] Dummy injection order (row numbers) created
INFO [2026-04-17 05:16:22] Merging objects with unequal amounts of samples.
INFO [2026-04-17 05:16:22] Samples only in first object:
INFO [2026-04-17 05:16:22] ID_666

INFO [2026-04-17 05:16:22] Samples only in second object:
INFO [2026-04-17 05:16:22] 

INFO [2026-04-17 05:16:22] Injection order differs between modes.Creating dummy injection order
INFO [2026-04-17 05:16:22] Dummy injection order (row numbers) created
INFO [2026-04-17 05:16:22] Merging objects with unequal amounts of samples.
INFO [2026-04-17 05:16:22] Samples only in first object:
INFO [2026-04-17 05:16:22] ID_666, Demo_22

INFO [2026-04-17 05:16:22] Samples only in second object:
INFO [2026-04-17 05:16:22] ID_999

INFO [2026-04-17 05:16:23] Starting logging
INFO [2026-04-17 05:16:23] Finished analysis. Fri Apr 17 05:16:23 2026
Session info:

INFO [2026-04-17 05:16:23] R Under development (unstable) (2025-02-19 r87757)
INFO [2026-04-17 05:16:23] Platform: aarch64-unknown-linux-gnu
INFO [2026-04-17 05:16:23] Running under: openEuler 24.03 (LTS-SP1)
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] Matrix products: default
INFO [2026-04-17 05:16:23] BLAS:   /home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so 
INFO [2026-04-17 05:16:23] LAPACK: /home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so;  LAPACK version 3.12.0
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] locale:
INFO [2026-04-17 05:16:23]  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
INFO [2026-04-17 05:16:23]  [3] LC_TIME=en_GB              LC_COLLATE=C              
INFO [2026-04-17 05:16:23]  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
INFO [2026-04-17 05:16:23]  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
INFO [2026-04-17 05:16:23]  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
INFO [2026-04-17 05:16:23] [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] time zone: UTC
INFO [2026-04-17 05:16:23] tzcode source: system (glibc)
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] attached base packages:
INFO [2026-04-17 05:16:23] [1] stats4    stats     graphics  grDevices utils     datasets  methods  
INFO [2026-04-17 05:16:23] [8] base     
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] other attached packages:
INFO [2026-04-17 05:16:23]  [1] notame_1.1.4                SummarizedExperiment_1.41.1
INFO [2026-04-17 05:16:23]  [3] Biobase_2.71.0              GenomicRanges_1.63.2       
INFO [2026-04-17 05:16:23]  [5] Seqinfo_1.1.0               IRanges_2.45.0             
INFO [2026-04-17 05:16:23]  [7] S4Vectors_0.49.1            BiocGenerics_0.57.0        
INFO [2026-04-17 05:16:23]  [9] generics_0.1.3              MatrixGenerics_1.23.0      
INFO [2026-04-17 05:16:23] [11] matrixStats_1.5.0           ggplot2_4.0.0              
INFO [2026-04-17 05:16:23] [13] testthat_3.2.3             
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] loaded via a namespace (and not attached):
INFO [2026-04-17 05:16:23]  [1] Matrix_1.7-3         gtable_0.3.6         futile.logger_1.4.3 
INFO [2026-04-17 05:16:23]  [4] dplyr_1.1.4          compiler_4.5.0       brio_1.1.5          
INFO [2026-04-17 05:16:23]  [7] zip_2.3.2            Rcpp_1.0.14          tidyselect_1.2.1    
INFO [2026-04-17 05:16:23] [10] tidyr_1.3.1          scales_1.4.0         lattice_0.22-7      
INFO [2026-04-17 05:16:23] [13] XVector_0.51.0       R6_2.6.1             S4Arrays_1.11.1     
INFO [2026-04-17 05:16:23] [16] openxlsx_4.2.8       tibble_3.2.1         DelayedArray_0.37.1 
INFO [2026-04-17 05:16:23] [19] desc_1.4.3           pillar_1.10.2        RColorBrewer_1.1-3  
INFO [2026-04-17 05:16:23] [22] rlang_1.1.6          stringi_1.8.7        S7_0.2.0            
INFO [2026-04-17 05:16:23] [25] viridisLite_0.4.2    SparseArray_1.11.13  cli_3.6.4           
INFO [2026-04-17 05:16:23] [28] formatR_1.14         withr_3.0.2          magrittr_2.0.3      
INFO [2026-04-17 05:16:23] [31] futile.options_1.0.1 grid_4.5.0           lifecycle_1.0.4     
INFO [2026-04-17 05:16:23] [34] waldo_0.6.1          vctrs_0.6.5          glue_1.8.0          
INFO [2026-04-17 05:16:23] [37] lambda.r_1.2.4       farver_2.1.2         abind_1.4-8         
INFO [2026-04-17 05:16:23] [40] purrr_1.0.4          tools_4.5.0          pkgconfig_2.0.3     
INFO [2026-04-17 05:16:23] New line
INFO [2026-04-17 05:16:23] Starting logging
INFO [2026-04-17 05:16:23] New line
INFO [2026-04-17 05:16:23] Finished analysis. Fri Apr 17 05:16:23 2026
Session info:

INFO [2026-04-17 05:16:23] R Under development (unstable) (2025-02-19 r87757)
INFO [2026-04-17 05:16:23] Platform: aarch64-unknown-linux-gnu
INFO [2026-04-17 05:16:23] Running under: openEuler 24.03 (LTS-SP1)
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] Matrix products: default
INFO [2026-04-17 05:16:23] BLAS:   /home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so 
INFO [2026-04-17 05:16:23] LAPACK: /home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so;  LAPACK version 3.12.0
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] locale:
INFO [2026-04-17 05:16:23]  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
INFO [2026-04-17 05:16:23]  [3] LC_TIME=en_GB              LC_COLLATE=C              
INFO [2026-04-17 05:16:23]  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
INFO [2026-04-17 05:16:23]  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
INFO [2026-04-17 05:16:23]  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
INFO [2026-04-17 05:16:23] [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] time zone: UTC
INFO [2026-04-17 05:16:23] tzcode source: system (glibc)
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] attached base packages:
INFO [2026-04-17 05:16:23] [1] stats4    stats     graphics  grDevices utils     datasets  methods  
INFO [2026-04-17 05:16:23] [8] base     
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] other attached packages:
INFO [2026-04-17 05:16:23]  [1] notame_1.1.4                SummarizedExperiment_1.41.1
INFO [2026-04-17 05:16:23]  [3] Biobase_2.71.0              GenomicRanges_1.63.2       
INFO [2026-04-17 05:16:23]  [5] Seqinfo_1.1.0               IRanges_2.45.0             
INFO [2026-04-17 05:16:23]  [7] S4Vectors_0.49.1            BiocGenerics_0.57.0        
INFO [2026-04-17 05:16:23]  [9] generics_0.1.3              MatrixGenerics_1.23.0      
INFO [2026-04-17 05:16:23] [11] matrixStats_1.5.0           ggplot2_4.0.0              
INFO [2026-04-17 05:16:23] [13] testthat_3.2.3             
INFO [2026-04-17 05:16:23] 
INFO [2026-04-17 05:16:23] loaded via a namespace (and not attached):
INFO [2026-04-17 05:16:23]  [1] Matrix_1.7-3         gtable_0.3.6         futile.logger_1.4.3 
INFO [2026-04-17 05:16:23]  [4] dplyr_1.1.4          compiler_4.5.0       brio_1.1.5          
INFO [2026-04-17 05:16:23]  [7] zip_2.3.2            Rcpp_1.0.14          tidyselect_1.2.1    
INFO [2026-04-17 05:16:23] [10] tidyr_1.3.1          scales_1.4.0         lattice_0.22-7      
INFO [2026-04-17 05:16:23] [13] XVector_0.51.0       R6_2.6.1             S4Arrays_1.11.1     
INFO [2026-04-17 05:16:23] [16] openxlsx_4.2.8       tibble_3.2.1         DelayedArray_0.37.1 
INFO [2026-04-17 05:16:23] [19] desc_1.4.3           pillar_1.10.2        RColorBrewer_1.1-3  
INFO [2026-04-17 05:16:23] [22] rlang_1.1.6          stringi_1.8.7        S7_0.2.0            
INFO [2026-04-17 05:16:23] [25] viridisLite_0.4.2    SparseArray_1.11.13  cli_3.6.4           
INFO [2026-04-17 05:16:23] [28] formatR_1.14         withr_3.0.2          magrittr_2.0.3      
INFO [2026-04-17 05:16:23] [31] futile.options_1.0.1 grid_4.5.0           lifecycle_1.0.4     
INFO [2026-04-17 05:16:23] [34] waldo_0.6.1          vctrs_0.6.5          glue_1.8.0          
INFO [2026-04-17 05:16:23] [37] lambda.r_1.2.4       farver_2.1.2         abind_1.4-8         
INFO [2026-04-17 05:16:23] [40] purrr_1.0.4          tools_4.5.0          pkgconfig_2.0.3     
INFO [2026-04-17 05:16:23] New line
INFO [2026-04-17 05:16:24] 
Starting random forest imputation at 2026-04-17 05:16:24.0175
INFO [2026-04-17 05:16:33] Out-of-bag error in random forest imputation: 0.47
INFO [2026-04-17 05:16:33] Random forest imputation finished at 2026-04-17 05:16:33.447416 

INFO [2026-04-17 05:16:33] 
Starting random forest imputation at 2026-04-17 05:16:33.803098
INFO [2026-04-17 05:16:40] Out-of-bag error in random forest imputation: 0.47
INFO [2026-04-17 05:16:40] Random forest imputation finished at 2026-04-17 05:16:40.509908 

INFO [2026-04-17 05:16:40] 
Starting random forest imputation at 2026-04-17 05:16:40.530981
INFO [2026-04-17 05:16:44] Out-of-bag error in random forest imputation: 0.47
INFO [2026-04-17 05:16:44] Random forest imputation finished at 2026-04-17 05:16:44.882043 

INFO [2026-04-17 05:16:44] 
Starting random forest imputation at 2026-04-17 05:16:44.988063
INFO [2026-04-17 05:16:50] Out-of-bag error in random forest imputation: 0.469
INFO [2026-04-17 05:16:50] Random forest imputation finished at 2026-04-17 05:16:50.911537 

INFO [2026-04-17 05:16:51] Starting PQN normalization
INFO [2026-04-17 05:16:51] Using median of qc samples as reference spectrum
INFO [2026-04-17 05:16:51] Starting PQN normalization
INFO [2026-04-17 05:16:51] Using median of all samples as reference spectrum
INFO [2026-04-17 05:16:51] Starting PQN normalization
INFO [2026-04-17 05:16:51] Using mean of qc samples as reference spectrum
INFO [2026-04-17 05:16:51] Starting PQN normalization
INFO [2026-04-17 05:16:51] Using mean of all samples as reference spectrum
INFO [2026-04-17 05:16:51] 
92% of features flagged for low quality
INFO [2026-04-17 05:16:51] Starting PQN normalization
INFO [2026-04-17 05:16:52] Using median of qc samples as reference spectrum
INFO [2026-04-17 05:16:52] Starting drift correction
INFO [2026-04-17 05:16:52] Zero values in feature abundances detected. Zeroes will be replaced with 1.1.
INFO [2026-04-17 05:16:55] Recomputing quality metrics for drift corrected data
INFO [2026-04-17 05:16:55] Drift correction performed
INFO [2026-04-17 05:16:55] Inspecting drift correction results
INFO [2026-04-17 05:16:55] Original quality metrics missing, recomputing
INFO [2026-04-17 05:16:55] Drift correction results inspected: Drift_corrected: 100%
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 85 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 85 ]
> 
> proc.time()
   user  system elapsed 
 46.815   3.004  49.547

Example timings

notame.Rcheck/notame-Ex.timings

nameusersystemelapsed
assess_quality0.2560.0160.273
citations0.4060.0120.418
cluster_features0.2950.0240.320
combined_data0.0560.0160.072
compress_clusters0.2040.0040.208
correct_drift3.7370.3543.893
drop_flagged0.1690.0080.177
drop_qcs0.0440.0080.051
finish_log0.0380.0070.047
fix_MSMS0.1420.0080.150
fix_object0.1490.0240.174
flag0.0320.0040.036
flag_contaminants0.2540.0640.319
flag_detection0.3000.0400.342
flag_quality0.3060.0120.318
flag_report0.4690.0240.495
import_from_excel0.3690.0160.390
import_from_msdial000
impute_rf4.2580.1284.395
impute_simple0.130.000.13
init_log0.0040.0000.004
inverse_normalize0.0490.0190.068
join_colData0.0410.0090.050
join_rowData0.0370.0000.037
log_text0.0030.0040.006
mark_nas0.0410.0110.053
merge_notame_sets0.6880.0640.755
pca_bhattacharyya_dist2.4130.1002.519
perform_repeatability0.1550.0040.159
pqn_normalization0.0930.0000.094
quality0.1210.0040.124
ruvs_qc0.2040.0080.211
write_to_excel0.2470.0080.255