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This page was generated on 2025-10-15 12:03 -0400 (Wed, 15 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4866
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4653
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4598
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 1463/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
notame 0.99.7  (landing page)
Vilhelm Suksi
Snapshot Date: 2025-10-14 13:45 -0400 (Tue, 14 Oct 2025)
git_url: https://git.bioconductor.org/packages/notame
git_branch: devel
git_last_commit: 4cc3f9f
git_last_commit_date: 2025-10-14 06:19:32 -0400 (Tue, 14 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for notame on nebbiolo2

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.

raw results


Summary

Package: notame
Version: 0.99.7
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_0.99.7.tar.gz
StartedAt: 2025-10-15 02:30:10 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 02:37:02 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 412.4 seconds
RetCode: 0
Status:   OK  
CheckDir: notame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_0.99.7.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 ‘0.99.7’
* 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 6.180  0.506   6.687
impute_rf              5.209  0.118   5.326
* 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.

Installation output

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 ‘0.99.7’
** 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)

Tests output

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 [2025-10-15 02:33:46] Pheno data was cleaned
INFO [2025-10-15 02:33:46] Checking provided sample ID column
INFO [2025-10-15 02:33:46] Column 'Sample_ID' created from id
INFO [2025-10-15 02:33:46] Pheno data was cleaned
INFO [2025-10-15 02:33:46] Sample ID generated from injection orders and prefix ID_
INFO [2025-10-15 02:33:46] Pheno data was cleaned
INFO [2025-10-15 02:33:46] Pheno data was cleaned
INFO [2025-10-15 02:33:46] Adding running index to 'QC' sample IDs
INFO [2025-10-15 02:33:46] Pheno data was cleaned
INFO [2025-10-15 02:33:46] Initializing 'Flag' column with unflagged features
INFO [2025-10-15 02:33:46] Assigning HILIC_pos as the value of the Split column for each feature
INFO [2025-10-15 02:33:46] Feature data was cleaned
INFO [2025-10-15 02:33:46] Initializing 'Flag' column with unflagged features
INFO [2025-10-15 02:33:46] Feature_ID column not found, creating feature IDs
INFO [2025-10-15 02:33:46] Initializing 'Flag' column with unflagged features
INFO [2025-10-15 02:33:46] Feature_ID column not found, creating feature IDs
INFO [2025-10-15 02:33:46] Initializing 'Flag' column with unflagged features
INFO [2025-10-15 02:33:46] Feature_ID column not found, creating feature IDs
INFO [2025-10-15 02:33:46] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 02:33:46] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 02:33:46] Creating feature IDs from Split, m/z and retention time
INFO [2025-10-15 02:33:46] Feature data was cleaned
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Creating feature IDs from Split, m/z and retention time
INFO [2025-10-15 02:33:46] Corner detected correctly at row 4, column D
INFO [2025-10-15 02:33:46] 
Extracting sample information from rows 1 to 4 and columns E to P
INFO [2025-10-15 02:33:46] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-15 02:33:46] Naming the last column of sample information "easy_Datafile"
INFO [2025-10-15 02:33:46] 
Extracting feature information from rows 5 to 14 and columns A to D
INFO [2025-10-15 02:33:46] 
Extracting feature abundances from rows 5 to 14 and columns E to P
INFO [2025-10-15 02:33:46] Sample ID generated from injection orders and prefix TEST_
INFO [2025-10-15 02:33:46] Pheno data was cleaned
INFO [2025-10-15 02:33:46] Initializing 'Flag' column with unflagged features
INFO [2025-10-15 02:33:46] Assigning easy as the value of the Split column for each feature
INFO [2025-10-15 02:33:46] Feature_ID column not found, creating feature IDs
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Creating feature IDs from Split, m/z and retention time
INFO [2025-10-15 02:33:46] Feature data was cleaned
INFO [2025-10-15 02:33:46] 
Checking sample information
INFO [2025-10-15 02:33:46] Checking 'Injection_order' column in feature data
INFO [2025-10-15 02:33:46] Checking 'Sample_ID' column in pheno data
INFO [2025-10-15 02:33:46] Checking 'QC' column in feature data
INFO [2025-10-15 02:33:46] Checking that feature abundances only contain numeric values
INFO [2025-10-15 02:33:46] 
Checking feature information
INFO [2025-10-15 02:33:46] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-15 02:33:46] Checking that m/z and retention time values are reasonable.
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Checking that feature data includes a 'Split' column
INFO [2025-10-15 02:33:46] Checking that feature data includes a 'Flag' column
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Creating feature IDs from Split, m/z and retention time
INFO [2025-10-15 02:33:46] Corner detected correctly at row 4, column F
INFO [2025-10-15 02:33:46] 
Extracting sample information from rows 1 to 4 and columns G to R
INFO [2025-10-15 02:33:46] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-15 02:33:46] Naming the last column of sample information "Datafile"
INFO [2025-10-15 02:33:46] 
Extracting feature information from rows 5 to 20 and columns A to F
INFO [2025-10-15 02:33:46] 
Extracting feature abundances from rows 5 to 20 and columns G to R
INFO [2025-10-15 02:33:46] Sample ID generated from injection orders and prefix TEST_
INFO [2025-10-15 02:33:46] Pheno data was cleaned
INFO [2025-10-15 02:33:46] Initializing 'Flag' column with unflagged features
INFO [2025-10-15 02:33:46] Creating Split column from Column, Mode
INFO [2025-10-15 02:33:46] Feature_ID column not found, creating feature IDs
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Creating feature IDs from Split, m/z and retention time
INFO [2025-10-15 02:33:46] Feature data was cleaned
INFO [2025-10-15 02:33:46] 
Checking sample information
INFO [2025-10-15 02:33:46] Checking 'Injection_order' column in feature data
INFO [2025-10-15 02:33:46] Checking 'Sample_ID' column in pheno data
INFO [2025-10-15 02:33:46] Checking 'QC' column in feature data
INFO [2025-10-15 02:33:46] Checking that feature abundances only contain numeric values
INFO [2025-10-15 02:33:46] 
Checking feature information
INFO [2025-10-15 02:33:46] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-15 02:33:46] Checking that m/z and retention time values are reasonable.
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-15 02:33:46] Checking that feature data includes a 'Split' column
INFO [2025-10-15 02:33:46] Checking that feature data includes a 'Flag' column
INFO [2025-10-15 02:33:47] Pheno data was cleaned
INFO [2025-10-15 02:33:47] Feature data was cleaned
INFO [2025-10-15 02:33:47] Pheno data was cleaned
INFO [2025-10-15 02:33:47] Feature data was cleaned
INFO [2025-10-15 02:33:47] Detecting corner position
INFO [2025-10-15 02:33:47] Corner detected correctly at row 11, column H
INFO [2025-10-15 02:33:47] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-10-15 02:33:47] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-15 02:33:47] Naming the last column of sample information "hilic_neg_Datafile"
INFO [2025-10-15 02:33:47] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-10-15 02:33:47] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-10-15 02:33:47] Pheno data was cleaned
INFO [2025-10-15 02:33:47] Feature data was cleaned
INFO [2025-10-15 02:33:47] 
Checking sample information
INFO [2025-10-15 02:33:47] Checking 'Injection_order' column in feature data
INFO [2025-10-15 02:33:47] Checking 'Sample_ID' column in pheno data
INFO [2025-10-15 02:33:47] Checking 'QC' column in feature data
INFO [2025-10-15 02:33:47] Checking that feature abundances only contain numeric values
INFO [2025-10-15 02:33:47] 
Checking feature information
INFO [2025-10-15 02:33:47] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-15 02:33:47] Checking that m/z and retention time values are reasonable.
INFO [2025-10-15 02:33:47] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 02:33:47] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 02:33:47] Checking that feature data includes a 'Split' column
INFO [2025-10-15 02:33:47] Checking that feature data includes a 'Flag' column
INFO [2025-10-15 02:33:47] Detecting corner position
INFO [2025-10-15 02:33:47] Corner detected correctly at row 11, column H
INFO [2025-10-15 02:33:47] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-10-15 02:33:47] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-15 02:33:47] Naming the last column of sample information "hilic_pos_Datafile"
INFO [2025-10-15 02:33:47] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-10-15 02:33:47] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-10-15 02:33:47] Pheno data was cleaned
INFO [2025-10-15 02:33:47] Feature data was cleaned
INFO [2025-10-15 02:33:47] 
Checking sample information
INFO [2025-10-15 02:33:47] Checking 'Injection_order' column in feature data
INFO [2025-10-15 02:33:47] Checking 'Sample_ID' column in pheno data
INFO [2025-10-15 02:33:47] Checking 'QC' column in feature data
INFO [2025-10-15 02:33:47] Checking that feature abundances only contain numeric values
INFO [2025-10-15 02:33:47] 
Checking feature information
INFO [2025-10-15 02:33:47] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-15 02:33:47] Checking that m/z and retention time values are reasonable.
INFO [2025-10-15 02:33:47] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 02:33:47] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 02:33:47] Checking that feature data includes a 'Split' column
INFO [2025-10-15 02:33:47] Checking that feature data includes a 'Flag' column
INFO [2025-10-15 02:33:47] Detecting corner position
INFO [2025-10-15 02:33:47] Corner detected correctly at row 11, column H
INFO [2025-10-15 02:33:47] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-10-15 02:33:47] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-15 02:33:47] Naming the last column of sample information "rp_neg_Datafile"
INFO [2025-10-15 02:33:47] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-10-15 02:33:47] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-10-15 02:33:47] Pheno data was cleaned
INFO [2025-10-15 02:33:47] Feature data was cleaned
INFO [2025-10-15 02:33:47] 
Checking sample information
INFO [2025-10-15 02:33:47] Checking 'Injection_order' column in feature data
INFO [2025-10-15 02:33:47] Checking 'Sample_ID' column in pheno data
INFO [2025-10-15 02:33:47] Checking 'QC' column in feature data
INFO [2025-10-15 02:33:47] Checking that feature abundances only contain numeric values
INFO [2025-10-15 02:33:47] 
Checking feature information
INFO [2025-10-15 02:33:47] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-15 02:33:47] Checking that m/z and retention time values are reasonable.
INFO [2025-10-15 02:33:47] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 02:33:47] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 02:33:47] Checking that feature data includes a 'Split' column
INFO [2025-10-15 02:33:47] Checking that feature data includes a 'Flag' column
INFO [2025-10-15 02:33:47] Detecting corner position
INFO [2025-10-15 02:33:47] Corner detected correctly at row 11, column H
INFO [2025-10-15 02:33:47] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-10-15 02:33:47] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-15 02:33:47] Naming the last column of sample information "rp_pos_Datafile"
INFO [2025-10-15 02:33:47] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-10-15 02:33:47] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-10-15 02:33:47] Pheno data was cleaned
INFO [2025-10-15 02:33:47] Feature data was cleaned
INFO [2025-10-15 02:33:47] 
Checking sample information
INFO [2025-10-15 02:33:47] Checking 'Injection_order' column in feature data
INFO [2025-10-15 02:33:47] Checking 'Sample_ID' column in pheno data
INFO [2025-10-15 02:33:47] Checking 'QC' column in feature data
INFO [2025-10-15 02:33:47] Checking that feature abundances only contain numeric values
INFO [2025-10-15 02:33:47] 
Checking feature information
INFO [2025-10-15 02:33:47] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-15 02:33:47] Checking that m/z and retention time values are reasonable.
INFO [2025-10-15 02:33:47] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 02:33:47] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 02:33:47] Checking that feature data includes a 'Split' column
INFO [2025-10-15 02:33:47] Checking that feature data includes a 'Flag' column
INFO [2025-10-15 02:33:47] Injection order differs between modes.Creating dummy injection order
INFO [2025-10-15 02:33:48] Dummy injection order (row numbers) created
INFO [2025-10-15 02:33:48] Merging objects with unequal amounts of samples.
INFO [2025-10-15 02:33:48] Samples only in first object:
INFO [2025-10-15 02:33:48] ID_666

INFO [2025-10-15 02:33:48] Samples only in second object:
INFO [2025-10-15 02:33:48] Demo_2

INFO [2025-10-15 02:33:48] Injection order differs between modes.Creating dummy injection order
INFO [2025-10-15 02:33:48] Dummy injection order (row numbers) created
INFO [2025-10-15 02:33:48] Merging objects with unequal amounts of samples.
INFO [2025-10-15 02:33:48] Samples only in first object:
INFO [2025-10-15 02:33:48] ID_666

INFO [2025-10-15 02:33:48] Samples only in second object:
INFO [2025-10-15 02:33:48] 

INFO [2025-10-15 02:33:48] Injection order differs between modes.Creating dummy injection order
INFO [2025-10-15 02:33:48] Dummy injection order (row numbers) created
INFO [2025-10-15 02:33:48] Merging objects with unequal amounts of samples.
INFO [2025-10-15 02:33:48] Samples only in first object:
INFO [2025-10-15 02:33:48] ID_666, Demo_22

INFO [2025-10-15 02:33:48] Samples only in second object:
INFO [2025-10-15 02:33:48] ID_999

INFO [2025-10-15 02:33:48] Starting logging
INFO [2025-10-15 02:33:48] Finished analysis. Wed Oct 15 02:33:48 2025
Session info:

INFO [2025-10-15 02:33:48] R version 4.5.1 Patched (2025-08-23 r88802)
INFO [2025-10-15 02:33:48] Platform: x86_64-pc-linux-gnu
INFO [2025-10-15 02:33:48] Running under: Ubuntu 24.04.3 LTS
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] Matrix products: default
INFO [2025-10-15 02:33:48] BLAS:   /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so 
INFO [2025-10-15 02:33:48] LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] locale:
INFO [2025-10-15 02:33:48]  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
INFO [2025-10-15 02:33:48]  [3] LC_TIME=en_GB              LC_COLLATE=C              
INFO [2025-10-15 02:33:48]  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
INFO [2025-10-15 02:33:48]  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
INFO [2025-10-15 02:33:48]  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
INFO [2025-10-15 02:33:48] [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] time zone: America/New_York
INFO [2025-10-15 02:33:48] tzcode source: system (glibc)
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] attached base packages:
INFO [2025-10-15 02:33:48] [1] stats4    stats     graphics  grDevices utils     datasets  methods  
INFO [2025-10-15 02:33:48] [8] base     
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] other attached packages:
INFO [2025-10-15 02:33:48]  [1] notame_0.99.7               SummarizedExperiment_1.39.2
INFO [2025-10-15 02:33:48]  [3] Biobase_2.69.1              GenomicRanges_1.61.5       
INFO [2025-10-15 02:33:48]  [5] Seqinfo_0.99.2              IRanges_2.43.5             
INFO [2025-10-15 02:33:48]  [7] S4Vectors_0.47.4            BiocGenerics_0.55.3        
INFO [2025-10-15 02:33:48]  [9] generics_0.1.4              MatrixGenerics_1.21.0      
INFO [2025-10-15 02:33:48] [11] matrixStats_1.5.0           ggplot2_4.0.0              
INFO [2025-10-15 02:33:48] [13] testthat_3.2.3             
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] loaded via a namespace (and not attached):
INFO [2025-10-15 02:33:48]  [1] Matrix_1.7-4         gtable_0.3.6         futile.logger_1.4.3 
INFO [2025-10-15 02:33:48]  [4] dplyr_1.1.4          compiler_4.5.1       crayon_1.5.3        
INFO [2025-10-15 02:33:48]  [7] brio_1.1.5           zip_2.3.3            Rcpp_1.1.0          
INFO [2025-10-15 02:33:48] [10] tidyselect_1.2.1     tidyr_1.3.1          scales_1.4.0        
INFO [2025-10-15 02:33:48] [13] lattice_0.22-7       R6_2.6.1             XVector_0.49.1      
INFO [2025-10-15 02:33:48] [16] S4Arrays_1.9.1       openxlsx_4.2.8       DelayedArray_0.35.3 
INFO [2025-10-15 02:33:48] [19] tibble_3.3.0         desc_1.4.3           pillar_1.11.1       
INFO [2025-10-15 02:33:48] [22] RColorBrewer_1.1-3   rlang_1.1.6          stringi_1.8.7       
INFO [2025-10-15 02:33:48] [25] S7_0.2.0             viridisLite_0.4.2    SparseArray_1.9.1   
INFO [2025-10-15 02:33:48] [28] cli_3.6.5            formatR_1.14         withr_3.0.2         
INFO [2025-10-15 02:33:48] [31] magrittr_2.0.4       futile.options_1.0.1 grid_4.5.1          
INFO [2025-10-15 02:33:48] [34] lifecycle_1.0.4      waldo_0.6.2          vctrs_0.6.5         
INFO [2025-10-15 02:33:48] [37] glue_1.8.0           lambda.r_1.2.4       farver_2.1.2        
INFO [2025-10-15 02:33:48] [40] abind_1.4-8          purrr_1.1.0          tools_4.5.1         
INFO [2025-10-15 02:33:48] [43] pkgconfig_2.0.3     
INFO [2025-10-15 02:33:48] New line
INFO [2025-10-15 02:33:48] Starting logging
INFO [2025-10-15 02:33:48] New line
INFO [2025-10-15 02:33:48] Finished analysis. Wed Oct 15 02:33:48 2025
Session info:

INFO [2025-10-15 02:33:48] R version 4.5.1 Patched (2025-08-23 r88802)
INFO [2025-10-15 02:33:48] Platform: x86_64-pc-linux-gnu
INFO [2025-10-15 02:33:48] Running under: Ubuntu 24.04.3 LTS
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] Matrix products: default
INFO [2025-10-15 02:33:48] BLAS:   /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so 
INFO [2025-10-15 02:33:48] LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] locale:
INFO [2025-10-15 02:33:48]  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
INFO [2025-10-15 02:33:48]  [3] LC_TIME=en_GB              LC_COLLATE=C              
INFO [2025-10-15 02:33:48]  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
INFO [2025-10-15 02:33:48]  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
INFO [2025-10-15 02:33:48]  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
INFO [2025-10-15 02:33:48] [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] time zone: America/New_York
INFO [2025-10-15 02:33:48] tzcode source: system (glibc)
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] attached base packages:
INFO [2025-10-15 02:33:48] [1] stats4    stats     graphics  grDevices utils     datasets  methods  
INFO [2025-10-15 02:33:48] [8] base     
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] other attached packages:
INFO [2025-10-15 02:33:48]  [1] notame_0.99.7               SummarizedExperiment_1.39.2
INFO [2025-10-15 02:33:48]  [3] Biobase_2.69.1              GenomicRanges_1.61.5       
INFO [2025-10-15 02:33:48]  [5] Seqinfo_0.99.2              IRanges_2.43.5             
INFO [2025-10-15 02:33:48]  [7] S4Vectors_0.47.4            BiocGenerics_0.55.3        
INFO [2025-10-15 02:33:48]  [9] generics_0.1.4              MatrixGenerics_1.21.0      
INFO [2025-10-15 02:33:48] [11] matrixStats_1.5.0           ggplot2_4.0.0              
INFO [2025-10-15 02:33:48] [13] testthat_3.2.3             
INFO [2025-10-15 02:33:48] 
INFO [2025-10-15 02:33:48] loaded via a namespace (and not attached):
INFO [2025-10-15 02:33:48]  [1] Matrix_1.7-4         gtable_0.3.6         futile.logger_1.4.3 
INFO [2025-10-15 02:33:48]  [4] dplyr_1.1.4          compiler_4.5.1       crayon_1.5.3        
INFO [2025-10-15 02:33:48]  [7] brio_1.1.5           zip_2.3.3            Rcpp_1.1.0          
INFO [2025-10-15 02:33:48] [10] tidyselect_1.2.1     tidyr_1.3.1          scales_1.4.0        
INFO [2025-10-15 02:33:48] [13] lattice_0.22-7       R6_2.6.1             XVector_0.49.1      
INFO [2025-10-15 02:33:48] [16] S4Arrays_1.9.1       openxlsx_4.2.8       DelayedArray_0.35.3 
INFO [2025-10-15 02:33:48] [19] tibble_3.3.0         desc_1.4.3           pillar_1.11.1       
INFO [2025-10-15 02:33:48] [22] RColorBrewer_1.1-3   rlang_1.1.6          stringi_1.8.7       
INFO [2025-10-15 02:33:48] [25] S7_0.2.0             viridisLite_0.4.2    SparseArray_1.9.1   
INFO [2025-10-15 02:33:48] [28] cli_3.6.5            formatR_1.14         withr_3.0.2         
INFO [2025-10-15 02:33:48] [31] magrittr_2.0.4       futile.options_1.0.1 grid_4.5.1          
INFO [2025-10-15 02:33:48] [34] lifecycle_1.0.4      waldo_0.6.2          vctrs_0.6.5         
INFO [2025-10-15 02:33:48] [37] glue_1.8.0           lambda.r_1.2.4       farver_2.1.2        
INFO [2025-10-15 02:33:48] [40] abind_1.4-8          purrr_1.1.0          tools_4.5.1         
INFO [2025-10-15 02:33:48] [43] pkgconfig_2.0.3     
INFO [2025-10-15 02:33:48] New line
INFO [2025-10-15 02:33:48] 
Starting random forest imputation at 2025-10-15 02:33:48.868812
INFO [2025-10-15 02:33:54] Out-of-bag error in random forest imputation: 0.469
INFO [2025-10-15 02:33:54] Random forest imputation finished at 2025-10-15 02:33:54.824448 

INFO [2025-10-15 02:33:55] 
Starting random forest imputation at 2025-10-15 02:33:55.071855
INFO [2025-10-15 02:33:58] Out-of-bag error in random forest imputation: 0.47
INFO [2025-10-15 02:33:58] Random forest imputation finished at 2025-10-15 02:33:58.735044 

INFO [2025-10-15 02:33:58] 
Starting random forest imputation at 2025-10-15 02:33:58.747684
INFO [2025-10-15 02:34:02] Out-of-bag error in random forest imputation: 0.47
INFO [2025-10-15 02:34:02] Random forest imputation finished at 2025-10-15 02:34:02.591361 

INFO [2025-10-15 02:34:02] 
Starting random forest imputation at 2025-10-15 02:34:02.631296
INFO [2025-10-15 02:34:07] Out-of-bag error in random forest imputation: 0.467
INFO [2025-10-15 02:34:07] Random forest imputation finished at 2025-10-15 02:34:07.72929 

INFO [2025-10-15 02:34:07] Starting PQN normalization
INFO [2025-10-15 02:34:08] Using median of qc samples as reference spectrum
INFO [2025-10-15 02:34:08] Starting PQN normalization
INFO [2025-10-15 02:34:08] Using median of all samples as reference spectrum
INFO [2025-10-15 02:34:08] Starting PQN normalization
INFO [2025-10-15 02:34:08] Using mean of qc samples as reference spectrum
INFO [2025-10-15 02:34:08] Starting PQN normalization
INFO [2025-10-15 02:34:08] Using mean of all samples as reference spectrum
INFO [2025-10-15 02:34:08] 
92% of features flagged for low quality
INFO [2025-10-15 02:34:08] Starting PQN normalization
INFO [2025-10-15 02:34:08] Using median of qc samples as reference spectrum
INFO [2025-10-15 02:34:08] Starting drift correction
INFO [2025-10-15 02:34:08] Zero values in feature abundances detected. Zeroes will be replaced with 1.1.
INFO [2025-10-15 02:34:11] Recomputing quality metrics for drift corrected data
INFO [2025-10-15 02:34:11] Drift correction performed
INFO [2025-10-15 02:34:11] Inspecting drift correction results
INFO [2025-10-15 02:34:11] Original quality metrics missing, recomputing
INFO [2025-10-15 02:34:12] Drift correction results inspected: Drift_corrected: 100%
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 84 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 84 ]
> 
> proc.time()
   user  system elapsed 
 33.897   1.331  34.895

Example timings

notame.Rcheck/notame-Ex.timings

nameusersystemelapsed
assess_quality0.1540.0220.177
citations0.3050.0030.309
cluster_features0.2480.0310.278
combined_data0.0390.0180.056
compress_clusters0.1500.0240.174
correct_drift2.9290.4033.183
drop_flagged0.1020.0210.123
drop_qcs0.0320.0050.037
finish_log0.0250.0090.036
fix_MSMS0.0960.0040.099
fix_object0.1190.0140.133
flag0.0270.0040.031
flag_contaminants0.1730.0100.183
flag_detection0.2170.0050.222
flag_quality0.2080.0190.227
flag_report0.2790.0050.284
import_from_excel0.2590.0190.279
impute_rf5.2090.1185.326
impute_simple0.0730.0090.083
init_log0.0030.0000.003
inverse_normalize0.0390.0020.040
join_colData0.0270.0040.031
join_rowData0.0230.0000.023
log_text0.0040.0000.004
mark_nas0.0330.0030.035
merge_notame_sets0.4590.0190.478
pca_bhattacharyya_dist6.1800.5066.687
perform_repeatability0.1590.0020.161
pqn_normalization0.0590.0020.061
quality0.0810.0020.083
ruvs_qc0.1540.0000.154
write_to_excel0.1690.0050.174