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This page was generated on 2025-11-28 11:38 -0500 (Fri, 28 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4866
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4614
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4571
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 1456/2328HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
notame 1.1.0  (landing page)
Vilhelm Suksi
Snapshot Date: 2025-11-27 13:40 -0500 (Thu, 27 Nov 2025)
git_url: https://git.bioconductor.org/packages/notame
git_branch: devel
git_last_commit: 778b063
git_last_commit_date: 2025-10-29 11:38:23 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    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

CHECK results for notame on lconway

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: 1.1.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:notame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings notame_1.1.0.tar.gz
StartedAt: 2025-11-28 03:23:20 -0500 (Fri, 28 Nov 2025)
EndedAt: 2025-11-28 03:27:54 -0500 (Fri, 28 Nov 2025)
EllapsedTime: 273.7 seconds
RetCode: 0
Status:   OK  
CheckDir: notame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:notame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings notame_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/notame.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘notame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘notame’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 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 7.837   0.83   8.714
* 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
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/notame.Rcheck/00check.log’
for details.

Installation output

notame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL notame
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘notame’ ...
** this is package ‘notame’ version ‘1.1.0’
** 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 Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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 [2025-11-28 03:27:22] Pheno data was cleaned
INFO [2025-11-28 03:27:22] Checking provided sample ID column
INFO [2025-11-28 03:27:22] Column 'Sample_ID' created from id
INFO [2025-11-28 03:27:22] Pheno data was cleaned
INFO [2025-11-28 03:27:22] Sample ID generated from injection orders and prefix ID_
INFO [2025-11-28 03:27:22] Pheno data was cleaned
INFO [2025-11-28 03:27:23] Pheno data was cleaned
INFO [2025-11-28 03:27:23] Adding running index to 'QC' sample IDs
INFO [2025-11-28 03:27:23] Pheno data was cleaned
INFO [2025-11-28 03:27:23] Initializing 'Flag' column with unflagged features
INFO [2025-11-28 03:27:23] Assigning HILIC_pos as the value of the Split column for each feature
INFO [2025-11-28 03:27:23] Feature data was cleaned
INFO [2025-11-28 03:27:23] Initializing 'Flag' column with unflagged features
INFO [2025-11-28 03:27:23] Feature_ID column not found, creating feature IDs
INFO [2025-11-28 03:27:23] Initializing 'Flag' column with unflagged features
INFO [2025-11-28 03:27:23] Feature_ID column not found, creating feature IDs
INFO [2025-11-28 03:27:23] Initializing 'Flag' column with unflagged features
INFO [2025-11-28 03:27:23] Feature_ID column not found, creating feature IDs
INFO [2025-11-28 03:27:23] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-28 03:27:23] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-28 03:27:23] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-28 03:27:23] Feature data was cleaned
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-28 03:27:23] Corner detected correctly at row 4, column D
INFO [2025-11-28 03:27:23] 
Extracting sample information from rows 1 to 4 and columns E to P
INFO [2025-11-28 03:27:23] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-28 03:27:23] Naming the last column of sample information "easy_Datafile"
INFO [2025-11-28 03:27:23] 
Extracting feature information from rows 5 to 14 and columns A to D
INFO [2025-11-28 03:27:23] 
Extracting feature abundances from rows 5 to 14 and columns E to P
INFO [2025-11-28 03:27:23] Sample ID generated from injection orders and prefix TEST_
INFO [2025-11-28 03:27:23] Pheno data was cleaned
INFO [2025-11-28 03:27:23] Initializing 'Flag' column with unflagged features
INFO [2025-11-28 03:27:23] Assigning easy as the value of the Split column for each feature
INFO [2025-11-28 03:27:23] Feature_ID column not found, creating feature IDs
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-28 03:27:23] Feature data was cleaned
INFO [2025-11-28 03:27:23] 
Checking sample information
INFO [2025-11-28 03:27:23] Checking 'Injection_order' column in feature data
INFO [2025-11-28 03:27:23] Checking 'Sample_ID' column in pheno data
INFO [2025-11-28 03:27:23] Checking 'QC' column in feature data
INFO [2025-11-28 03:27:23] Checking that feature abundances only contain numeric values
INFO [2025-11-28 03:27:23] 
Checking feature information
INFO [2025-11-28 03:27:23] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-28 03:27:23] Checking that m/z and retention time values are reasonable.
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Checking that feature data includes a 'Split' column
INFO [2025-11-28 03:27:23] Checking that feature data includes a 'Flag' column
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-28 03:27:23] Corner detected correctly at row 4, column F
INFO [2025-11-28 03:27:23] 
Extracting sample information from rows 1 to 4 and columns G to R
INFO [2025-11-28 03:27:23] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-28 03:27:23] Naming the last column of sample information "Datafile"
INFO [2025-11-28 03:27:23] 
Extracting feature information from rows 5 to 20 and columns A to F
INFO [2025-11-28 03:27:23] 
Extracting feature abundances from rows 5 to 20 and columns G to R
INFO [2025-11-28 03:27:23] Sample ID generated from injection orders and prefix TEST_
INFO [2025-11-28 03:27:23] Pheno data was cleaned
INFO [2025-11-28 03:27:23] Initializing 'Flag' column with unflagged features
INFO [2025-11-28 03:27:23] Creating Split column from Column, Mode
INFO [2025-11-28 03:27:23] Feature_ID column not found, creating feature IDs
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-28 03:27:23] Feature data was cleaned
INFO [2025-11-28 03:27:23] 
Checking sample information
INFO [2025-11-28 03:27:23] Checking 'Injection_order' column in feature data
INFO [2025-11-28 03:27:23] Checking 'Sample_ID' column in pheno data
INFO [2025-11-28 03:27:23] Checking 'QC' column in feature data
INFO [2025-11-28 03:27:23] Checking that feature abundances only contain numeric values
INFO [2025-11-28 03:27:23] 
Checking feature information
INFO [2025-11-28 03:27:23] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-28 03:27:23] Checking that m/z and retention time values are reasonable.
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-28 03:27:23] Checking that feature data includes a 'Split' column
INFO [2025-11-28 03:27:23] Checking that feature data includes a 'Flag' column
INFO [2025-11-28 03:27:24] Pheno data was cleaned
INFO [2025-11-28 03:27:24] Feature data was cleaned
INFO [2025-11-28 03:27:24] Pheno data was cleaned
INFO [2025-11-28 03:27:24] Feature data was cleaned
INFO [2025-11-28 03:27:24] Detecting corner position
INFO [2025-11-28 03:27:24] Corner detected correctly at row 11, column H
INFO [2025-11-28 03:27:24] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-28 03:27:24] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-28 03:27:24] Naming the last column of sample information "hilic_neg_Datafile"
INFO [2025-11-28 03:27:24] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-28 03:27:24] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-28 03:27:24] Pheno data was cleaned
INFO [2025-11-28 03:27:24] Feature data was cleaned
INFO [2025-11-28 03:27:24] 
Checking sample information
INFO [2025-11-28 03:27:24] Checking 'Injection_order' column in feature data
INFO [2025-11-28 03:27:24] Checking 'Sample_ID' column in pheno data
INFO [2025-11-28 03:27:24] Checking 'QC' column in feature data
INFO [2025-11-28 03:27:24] Checking that feature abundances only contain numeric values
INFO [2025-11-28 03:27:24] 
Checking feature information
INFO [2025-11-28 03:27:24] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-28 03:27:24] Checking that m/z and retention time values are reasonable.
INFO [2025-11-28 03:27:24] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-28 03:27:24] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-28 03:27:24] Checking that feature data includes a 'Split' column
INFO [2025-11-28 03:27:24] Checking that feature data includes a 'Flag' column
INFO [2025-11-28 03:27:24] Detecting corner position
INFO [2025-11-28 03:27:24] Corner detected correctly at row 11, column H
INFO [2025-11-28 03:27:24] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-28 03:27:24] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-28 03:27:24] Naming the last column of sample information "hilic_pos_Datafile"
INFO [2025-11-28 03:27:24] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-28 03:27:24] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-28 03:27:24] Pheno data was cleaned
INFO [2025-11-28 03:27:24] Feature data was cleaned
INFO [2025-11-28 03:27:24] 
Checking sample information
INFO [2025-11-28 03:27:24] Checking 'Injection_order' column in feature data
INFO [2025-11-28 03:27:24] Checking 'Sample_ID' column in pheno data
INFO [2025-11-28 03:27:24] Checking 'QC' column in feature data
INFO [2025-11-28 03:27:24] Checking that feature abundances only contain numeric values
INFO [2025-11-28 03:27:24] 
Checking feature information
INFO [2025-11-28 03:27:24] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-28 03:27:24] Checking that m/z and retention time values are reasonable.
INFO [2025-11-28 03:27:24] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-28 03:27:24] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-28 03:27:24] Checking that feature data includes a 'Split' column
INFO [2025-11-28 03:27:24] Checking that feature data includes a 'Flag' column
INFO [2025-11-28 03:27:24] Detecting corner position
INFO [2025-11-28 03:27:24] Corner detected correctly at row 11, column H
INFO [2025-11-28 03:27:24] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-28 03:27:24] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-28 03:27:24] Naming the last column of sample information "rp_neg_Datafile"
INFO [2025-11-28 03:27:24] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-28 03:27:24] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-28 03:27:24] Pheno data was cleaned
INFO [2025-11-28 03:27:24] Feature data was cleaned
INFO [2025-11-28 03:27:24] 
Checking sample information
INFO [2025-11-28 03:27:24] Checking 'Injection_order' column in feature data
INFO [2025-11-28 03:27:24] Checking 'Sample_ID' column in pheno data
INFO [2025-11-28 03:27:24] Checking 'QC' column in feature data
INFO [2025-11-28 03:27:24] Checking that feature abundances only contain numeric values
INFO [2025-11-28 03:27:24] 
Checking feature information
INFO [2025-11-28 03:27:24] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-28 03:27:24] Checking that m/z and retention time values are reasonable.
INFO [2025-11-28 03:27:24] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-28 03:27:24] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-28 03:27:24] Checking that feature data includes a 'Split' column
INFO [2025-11-28 03:27:24] Checking that feature data includes a 'Flag' column
INFO [2025-11-28 03:27:24] Detecting corner position
INFO [2025-11-28 03:27:24] Corner detected correctly at row 11, column H
INFO [2025-11-28 03:27:25] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-28 03:27:25] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-28 03:27:25] Naming the last column of sample information "rp_pos_Datafile"
INFO [2025-11-28 03:27:25] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-28 03:27:25] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-28 03:27:25] Pheno data was cleaned
INFO [2025-11-28 03:27:25] Feature data was cleaned
INFO [2025-11-28 03:27:25] 
Checking sample information
INFO [2025-11-28 03:27:25] Checking 'Injection_order' column in feature data
INFO [2025-11-28 03:27:25] Checking 'Sample_ID' column in pheno data
INFO [2025-11-28 03:27:25] Checking 'QC' column in feature data
INFO [2025-11-28 03:27:25] Checking that feature abundances only contain numeric values
INFO [2025-11-28 03:27:25] 
Checking feature information
INFO [2025-11-28 03:27:25] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-28 03:27:25] Checking that m/z and retention time values are reasonable.
INFO [2025-11-28 03:27:25] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-28 03:27:25] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-28 03:27:25] Checking that feature data includes a 'Split' column
INFO [2025-11-28 03:27:25] Checking that feature data includes a 'Flag' column
INFO [2025-11-28 03:27:25] Injection order differs between modes.Creating dummy injection order
INFO [2025-11-28 03:27:25] Dummy injection order (row numbers) created
INFO [2025-11-28 03:27:25] Merging objects with unequal amounts of samples.
INFO [2025-11-28 03:27:25] Samples only in first object:
INFO [2025-11-28 03:27:25] ID_666

INFO [2025-11-28 03:27:25] Samples only in second object:
INFO [2025-11-28 03:27:25] Demo_2

INFO [2025-11-28 03:27:25] Injection order differs between modes.Creating dummy injection order
INFO [2025-11-28 03:27:25] Dummy injection order (row numbers) created
INFO [2025-11-28 03:27:25] Merging objects with unequal amounts of samples.
INFO [2025-11-28 03:27:25] Samples only in first object:
INFO [2025-11-28 03:27:25] ID_666

INFO [2025-11-28 03:27:25] Samples only in second object:
INFO [2025-11-28 03:27:25] 

INFO [2025-11-28 03:27:26] Injection order differs between modes.Creating dummy injection order
INFO [2025-11-28 03:27:26] Dummy injection order (row numbers) created
INFO [2025-11-28 03:27:26] Merging objects with unequal amounts of samples.
INFO [2025-11-28 03:27:26] Samples only in first object:
INFO [2025-11-28 03:27:26] ID_666, Demo_22

INFO [2025-11-28 03:27:26] Samples only in second object:
INFO [2025-11-28 03:27:26] ID_999

INFO [2025-11-28 03:27:26] Starting logging
INFO [2025-11-28 03:27:26] Finished analysis. Fri Nov 28 03:27:26 2025
Session info:

INFO [2025-11-28 03:27:26] R Under development (unstable) (2025-10-21 r88958)
INFO [2025-11-28 03:27:26] Platform: x86_64-apple-darwin20
INFO [2025-11-28 03:27:26] Running under: macOS Ventura 13.7.8
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] Matrix products: default
INFO [2025-11-28 03:27:26] BLAS:   /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libRblas.0.dylib 
INFO [2025-11-28 03:27:26] LAPACK: /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] locale:
INFO [2025-11-28 03:27:26] [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] time zone: America/New_York
INFO [2025-11-28 03:27:26] tzcode source: internal
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] attached base packages:
INFO [2025-11-28 03:27:26] [1] stats4    stats     graphics  grDevices utils     datasets  methods  
INFO [2025-11-28 03:27:26] [8] base     
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] other attached packages:
INFO [2025-11-28 03:27:26]  [1] notame_1.1.0                SummarizedExperiment_1.41.0
INFO [2025-11-28 03:27:26]  [3] Biobase_2.71.0              GenomicRanges_1.63.0       
INFO [2025-11-28 03:27:26]  [5] Seqinfo_1.1.0               IRanges_2.45.0             
INFO [2025-11-28 03:27:26]  [7] S4Vectors_0.49.0            BiocGenerics_0.57.0        
INFO [2025-11-28 03:27:26]  [9] generics_0.1.4              MatrixGenerics_1.23.0      
INFO [2025-11-28 03:27:26] [11] matrixStats_1.5.0           ggplot2_4.0.1              
INFO [2025-11-28 03:27:26] [13] testthat_3.3.1             
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] loaded via a namespace (and not attached):
INFO [2025-11-28 03:27:26]  [1] tidyr_1.3.1          futile.options_1.0.1 SparseArray_1.11.6  
INFO [2025-11-28 03:27:26]  [4] stringi_1.8.7        lattice_0.22-7       magrittr_2.0.4      
INFO [2025-11-28 03:27:26]  [7] grid_4.6.0           RColorBrewer_1.1-3   Matrix_1.7-4        
INFO [2025-11-28 03:27:26] [10] zip_2.3.3            brio_1.1.5           formatR_1.14        
INFO [2025-11-28 03:27:26] [13] purrr_1.2.0          viridisLite_0.4.2    scales_1.4.0        
INFO [2025-11-28 03:27:26] [16] abind_1.4-8          cli_3.6.5            rlang_1.1.6         
INFO [2025-11-28 03:27:26] [19] XVector_0.51.0       futile.logger_1.4.3  withr_3.0.2         
INFO [2025-11-28 03:27:26] [22] DelayedArray_0.37.0  S4Arrays_1.11.1      tools_4.6.0         
INFO [2025-11-28 03:27:26] [25] dplyr_1.1.4          lambda.r_1.2.4       vctrs_0.6.5         
INFO [2025-11-28 03:27:26] [28] R6_2.6.1             lifecycle_1.0.4      pkgconfig_2.0.3     
INFO [2025-11-28 03:27:26] [31] waldo_0.6.2          desc_1.4.3           pillar_1.11.1       
INFO [2025-11-28 03:27:26] [34] openxlsx_4.2.8.1     gtable_0.3.6         glue_1.8.0          
INFO [2025-11-28 03:27:26] [37] Rcpp_1.1.0           tibble_3.3.0         tidyselect_1.2.1    
INFO [2025-11-28 03:27:26] [40] dichromat_2.0-0.1    farver_2.1.2         compiler_4.6.0      
INFO [2025-11-28 03:27:26] [43] S7_0.2.1            
INFO [2025-11-28 03:27:26] New line
INFO [2025-11-28 03:27:26] Starting logging
INFO [2025-11-28 03:27:26] New line
INFO [2025-11-28 03:27:26] Finished analysis. Fri Nov 28 03:27:26 2025
Session info:

INFO [2025-11-28 03:27:26] R Under development (unstable) (2025-10-21 r88958)
INFO [2025-11-28 03:27:26] Platform: x86_64-apple-darwin20
INFO [2025-11-28 03:27:26] Running under: macOS Ventura 13.7.8
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] Matrix products: default
INFO [2025-11-28 03:27:26] BLAS:   /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libRblas.0.dylib 
INFO [2025-11-28 03:27:26] LAPACK: /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] locale:
INFO [2025-11-28 03:27:26] [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] time zone: America/New_York
INFO [2025-11-28 03:27:26] tzcode source: internal
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] attached base packages:
INFO [2025-11-28 03:27:26] [1] stats4    stats     graphics  grDevices utils     datasets  methods  
INFO [2025-11-28 03:27:26] [8] base     
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] other attached packages:
INFO [2025-11-28 03:27:26]  [1] notame_1.1.0                SummarizedExperiment_1.41.0
INFO [2025-11-28 03:27:26]  [3] Biobase_2.71.0              GenomicRanges_1.63.0       
INFO [2025-11-28 03:27:26]  [5] Seqinfo_1.1.0               IRanges_2.45.0             
INFO [2025-11-28 03:27:26]  [7] S4Vectors_0.49.0            BiocGenerics_0.57.0        
INFO [2025-11-28 03:27:26]  [9] generics_0.1.4              MatrixGenerics_1.23.0      
INFO [2025-11-28 03:27:26] [11] matrixStats_1.5.0           ggplot2_4.0.1              
INFO [2025-11-28 03:27:26] [13] testthat_3.3.1             
INFO [2025-11-28 03:27:26] 
INFO [2025-11-28 03:27:26] loaded via a namespace (and not attached):
INFO [2025-11-28 03:27:26]  [1] tidyr_1.3.1          futile.options_1.0.1 SparseArray_1.11.6  
INFO [2025-11-28 03:27:26]  [4] stringi_1.8.7        lattice_0.22-7       magrittr_2.0.4      
INFO [2025-11-28 03:27:26]  [7] grid_4.6.0           RColorBrewer_1.1-3   Matrix_1.7-4        
INFO [2025-11-28 03:27:26] [10] zip_2.3.3            brio_1.1.5           formatR_1.14        
INFO [2025-11-28 03:27:26] [13] purrr_1.2.0          viridisLite_0.4.2    scales_1.4.0        
INFO [2025-11-28 03:27:26] [16] abind_1.4-8          cli_3.6.5            rlang_1.1.6         
INFO [2025-11-28 03:27:26] [19] XVector_0.51.0       futile.logger_1.4.3  withr_3.0.2         
INFO [2025-11-28 03:27:26] [22] DelayedArray_0.37.0  S4Arrays_1.11.1      tools_4.6.0         
INFO [2025-11-28 03:27:26] [25] dplyr_1.1.4          lambda.r_1.2.4       vctrs_0.6.5         
INFO [2025-11-28 03:27:26] [28] R6_2.6.1             lifecycle_1.0.4      pkgconfig_2.0.3     
INFO [2025-11-28 03:27:26] [31] waldo_0.6.2          desc_1.4.3           pillar_1.11.1       
INFO [2025-11-28 03:27:26] [34] openxlsx_4.2.8.1     gtable_0.3.6         glue_1.8.0          
INFO [2025-11-28 03:27:26] [37] Rcpp_1.1.0           tibble_3.3.0         tidyselect_1.2.1    
INFO [2025-11-28 03:27:26] [40] dichromat_2.0-0.1    farver_2.1.2         compiler_4.6.0      
INFO [2025-11-28 03:27:26] [43] S7_0.2.1            
INFO [2025-11-28 03:27:26] New line
INFO [2025-11-28 03:27:26] 
Starting random forest imputation at 2025-11-28 03:27:26.803011
INFO [2025-11-28 03:27:30] Out-of-bag error in random forest imputation: 0.467
INFO [2025-11-28 03:27:30] Random forest imputation finished at 2025-11-28 03:27:30.567553 

INFO [2025-11-28 03:27:30] 
Starting random forest imputation at 2025-11-28 03:27:30.889543
INFO [2025-11-28 03:27:33] Out-of-bag error in random forest imputation: 0.472
INFO [2025-11-28 03:27:33] Random forest imputation finished at 2025-11-28 03:27:33.715804 

INFO [2025-11-28 03:27:33] 
Starting random forest imputation at 2025-11-28 03:27:33.736171
INFO [2025-11-28 03:27:36] Out-of-bag error in random forest imputation: 0.469
INFO [2025-11-28 03:27:36] Random forest imputation finished at 2025-11-28 03:27:36.145512 

INFO [2025-11-28 03:27:36] 
Starting random forest imputation at 2025-11-28 03:27:36.202243
INFO [2025-11-28 03:27:38] Out-of-bag error in random forest imputation: 0.468
INFO [2025-11-28 03:27:38] Random forest imputation finished at 2025-11-28 03:27:38.58342 

INFO [2025-11-28 03:27:38] Starting PQN normalization
INFO [2025-11-28 03:27:38] Using median of qc samples as reference spectrum
INFO [2025-11-28 03:27:39] Starting PQN normalization
INFO [2025-11-28 03:27:39] Using median of all samples as reference spectrum
INFO [2025-11-28 03:27:39] Starting PQN normalization
INFO [2025-11-28 03:27:39] Using mean of qc samples as reference spectrum
INFO [2025-11-28 03:27:39] Starting PQN normalization
INFO [2025-11-28 03:27:39] Using mean of all samples as reference spectrum
INFO [2025-11-28 03:27:39] 
92% of features flagged for low quality
INFO [2025-11-28 03:27:39] Starting PQN normalization
INFO [2025-11-28 03:27:39] Using median of qc samples as reference spectrum
INFO [2025-11-28 03:27:39] Starting drift correction
INFO [2025-11-28 03:27:39] Zero values in feature abundances detected. Zeroes will be replaced with 1.1.
INFO [2025-11-28 03:27:42] Recomputing quality metrics for drift corrected data
INFO [2025-11-28 03:27:42] Drift correction performed
INFO [2025-11-28 03:27:42] Inspecting drift correction results
INFO [2025-11-28 03:27:42] Original quality metrics missing, recomputing
INFO [2025-11-28 03:27:43] 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 
 32.298   4.800  31.157

Example timings

notame.Rcheck/notame-Ex.timings

nameusersystemelapsed
assess_quality0.2080.0250.235
citations0.3280.0320.366
cluster_features0.2700.0430.317
combined_data0.0630.0330.096
compress_clusters0.1520.0220.174
correct_drift3.4540.3653.615
drop_flagged0.1280.0150.144
drop_qcs0.0470.0090.058
finish_log0.0300.0130.044
fix_MSMS0.1260.0200.147
fix_object0.1590.0180.178
flag0.0380.0110.049
flag_contaminants0.2350.0230.260
flag_detection0.2540.0140.270
flag_quality0.2460.0080.255
flag_report0.3480.0070.355
import_from_excel0.3080.0330.346
impute_rf3.0090.8142.552
impute_simple0.1040.0050.109
init_log0.0030.0010.005
inverse_normalize0.0500.0040.054
join_colData0.0330.0030.036
join_rowData0.0280.0040.033
log_text0.0040.0010.005
mark_nas0.0390.0040.043
merge_notame_sets0.5540.0100.567
pca_bhattacharyya_dist7.8370.8308.714
perform_repeatability0.2210.0070.231
pqn_normalization0.0750.0060.080
quality0.1090.0100.119
ruvs_qc0.2170.0240.242
write_to_excel0.2650.0500.323