Build/check report for BioC 3.23 - CHECK results for notame on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4821
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*

CHECK results for notame on nebbiolo1

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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:notame.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings notame_1.1.0.tar.gz

StartedAt: 2025-11-08 02:04:25 -0500 (Sat, 08 Nov 2025)

EndedAt: 2025-11-08 02:11:07 -0500 (Sat, 08 Nov 2025)

EllapsedTime: 401.6 seconds

RetCode: 0

Status: OK

CheckDir: notame.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:notame.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings notame_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/notame.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘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 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 6.552  0.776   7.328
* 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-3.23-bioc/meat/notame.Rcheck/00check.log’
for details.

Installation output

notame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL notame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2025-10-20 r88955) -- "Unsuffered Consequences"
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 [2025-11-08 02:07:56] Pheno data was cleaned
INFO [2025-11-08 02:07:56] Checking provided sample ID column
INFO [2025-11-08 02:07:56] Column 'Sample_ID' created from id
INFO [2025-11-08 02:07:56] Pheno data was cleaned
INFO [2025-11-08 02:07:56] Sample ID generated from injection orders and prefix ID_
INFO [2025-11-08 02:07:56] Pheno data was cleaned
INFO [2025-11-08 02:07:56] Pheno data was cleaned
INFO [2025-11-08 02:07:56] Adding running index to 'QC' sample IDs
INFO [2025-11-08 02:07:56] Pheno data was cleaned
INFO [2025-11-08 02:07:56] Initializing 'Flag' column with unflagged features
INFO [2025-11-08 02:07:56] Assigning HILIC_pos as the value of the Split column for each feature
INFO [2025-11-08 02:07:56] Feature data was cleaned
INFO [2025-11-08 02:07:56] Initializing 'Flag' column with unflagged features
INFO [2025-11-08 02:07:56] Feature_ID column not found, creating feature IDs
INFO [2025-11-08 02:07:56] Initializing 'Flag' column with unflagged features
INFO [2025-11-08 02:07:56] Feature_ID column not found, creating feature IDs
INFO [2025-11-08 02:07:56] Initializing 'Flag' column with unflagged features
INFO [2025-11-08 02:07:56] Feature_ID column not found, creating feature IDs
INFO [2025-11-08 02:07:56] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-08 02:07:56] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-08 02:07:56] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-08 02:07:56] Feature data was cleaned
INFO [2025-11-08 02:07:56] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:56] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:56] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-08 02:07:56] Corner detected correctly at row 4, column D
INFO [2025-11-08 02:07:56] 
Extracting sample information from rows 1 to 4 and columns E to P
INFO [2025-11-08 02:07:56] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-08 02:07:56] Naming the last column of sample information "easy_Datafile"
INFO [2025-11-08 02:07:56] 
Extracting feature information from rows 5 to 14 and columns A to D
INFO [2025-11-08 02:07:56] 
Extracting feature abundances from rows 5 to 14 and columns E to P
INFO [2025-11-08 02:07:56] Sample ID generated from injection orders and prefix TEST_
INFO [2025-11-08 02:07:56] Pheno data was cleaned
INFO [2025-11-08 02:07:56] Initializing 'Flag' column with unflagged features
INFO [2025-11-08 02:07:56] Assigning easy as the value of the Split column for each feature
INFO [2025-11-08 02:07:56] Feature_ID column not found, creating feature IDs
INFO [2025-11-08 02:07:56] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:56] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:56] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-08 02:07:56] Feature data was cleaned
INFO [2025-11-08 02:07:56] 
Checking sample information
INFO [2025-11-08 02:07:56] Checking 'Injection_order' column in feature data
INFO [2025-11-08 02:07:56] Checking 'Sample_ID' column in pheno data
INFO [2025-11-08 02:07:56] Checking 'QC' column in feature data
INFO [2025-11-08 02:07:56] Checking that feature abundances only contain numeric values
INFO [2025-11-08 02:07:56] 
Checking feature information
INFO [2025-11-08 02:07:56] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-08 02:07:56] Checking that m/z and retention time values are reasonable.
INFO [2025-11-08 02:07:56] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:56] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:56] Checking that feature data includes a 'Split' column
INFO [2025-11-08 02:07:56] Checking that feature data includes a 'Flag' column
INFO [2025-11-08 02:07:56] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:56] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:56] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-08 02:07:56] Corner detected correctly at row 4, column F
INFO [2025-11-08 02:07:56] 
Extracting sample information from rows 1 to 4 and columns G to R
INFO [2025-11-08 02:07:56] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-08 02:07:56] Naming the last column of sample information "Datafile"
INFO [2025-11-08 02:07:56] 
Extracting feature information from rows 5 to 20 and columns A to F
INFO [2025-11-08 02:07:56] 
Extracting feature abundances from rows 5 to 20 and columns G to R
INFO [2025-11-08 02:07:56] Sample ID generated from injection orders and prefix TEST_
INFO [2025-11-08 02:07:56] Pheno data was cleaned
INFO [2025-11-08 02:07:56] Initializing 'Flag' column with unflagged features
INFO [2025-11-08 02:07:56] Creating Split column from Column, Mode
INFO [2025-11-08 02:07:57] Feature_ID column not found, creating feature IDs
INFO [2025-11-08 02:07:57] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:57] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:57] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-08 02:07:57] Feature data was cleaned
INFO [2025-11-08 02:07:57] 
Checking sample information
INFO [2025-11-08 02:07:57] Checking 'Injection_order' column in feature data
INFO [2025-11-08 02:07:57] Checking 'Sample_ID' column in pheno data
INFO [2025-11-08 02:07:57] Checking 'QC' column in feature data
INFO [2025-11-08 02:07:57] Checking that feature abundances only contain numeric values
INFO [2025-11-08 02:07:57] 
Checking feature information
INFO [2025-11-08 02:07:57] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-08 02:07:57] Checking that m/z and retention time values are reasonable.
INFO [2025-11-08 02:07:57] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:57] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-08 02:07:57] Checking that feature data includes a 'Split' column
INFO [2025-11-08 02:07:57] Checking that feature data includes a 'Flag' column
INFO [2025-11-08 02:07:57] Pheno data was cleaned
INFO [2025-11-08 02:07:57] Feature data was cleaned
INFO [2025-11-08 02:07:57] Pheno data was cleaned
INFO [2025-11-08 02:07:57] Feature data was cleaned
INFO [2025-11-08 02:07:57] Detecting corner position
INFO [2025-11-08 02:07:57] Corner detected correctly at row 11, column H
INFO [2025-11-08 02:07:57] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-08 02:07:57] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-08 02:07:57] Naming the last column of sample information "hilic_neg_Datafile"
INFO [2025-11-08 02:07:57] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-08 02:07:57] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-08 02:07:57] Pheno data was cleaned
INFO [2025-11-08 02:07:57] Feature data was cleaned
INFO [2025-11-08 02:07:57] 
Checking sample information
INFO [2025-11-08 02:07:57] Checking 'Injection_order' column in feature data
INFO [2025-11-08 02:07:57] Checking 'Sample_ID' column in pheno data
INFO [2025-11-08 02:07:57] Checking 'QC' column in feature data
INFO [2025-11-08 02:07:57] Checking that feature abundances only contain numeric values
INFO [2025-11-08 02:07:57] 
Checking feature information
INFO [2025-11-08 02:07:57] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-08 02:07:57] Checking that m/z and retention time values are reasonable.
INFO [2025-11-08 02:07:57] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-08 02:07:57] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-08 02:07:57] Checking that feature data includes a 'Split' column
INFO [2025-11-08 02:07:57] Checking that feature data includes a 'Flag' column
INFO [2025-11-08 02:07:57] Detecting corner position
INFO [2025-11-08 02:07:57] Corner detected correctly at row 11, column H
INFO [2025-11-08 02:07:57] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-08 02:07:57] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-08 02:07:57] Naming the last column of sample information "hilic_pos_Datafile"
INFO [2025-11-08 02:07:57] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-08 02:07:57] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-08 02:07:57] Pheno data was cleaned
INFO [2025-11-08 02:07:57] Feature data was cleaned
INFO [2025-11-08 02:07:57] 
Checking sample information
INFO [2025-11-08 02:07:57] Checking 'Injection_order' column in feature data
INFO [2025-11-08 02:07:57] Checking 'Sample_ID' column in pheno data
INFO [2025-11-08 02:07:57] Checking 'QC' column in feature data
INFO [2025-11-08 02:07:57] Checking that feature abundances only contain numeric values
INFO [2025-11-08 02:07:57] 
Checking feature information
INFO [2025-11-08 02:07:57] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-08 02:07:57] Checking that m/z and retention time values are reasonable.
INFO [2025-11-08 02:07:57] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-08 02:07:57] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-08 02:07:57] Checking that feature data includes a 'Split' column
INFO [2025-11-08 02:07:57] Checking that feature data includes a 'Flag' column
INFO [2025-11-08 02:07:57] Detecting corner position
INFO [2025-11-08 02:07:57] Corner detected correctly at row 11, column H
INFO [2025-11-08 02:07:57] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-08 02:07:57] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-08 02:07:57] Naming the last column of sample information "rp_neg_Datafile"
INFO [2025-11-08 02:07:57] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-08 02:07:57] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-08 02:07:57] Pheno data was cleaned
INFO [2025-11-08 02:07:57] Feature data was cleaned
INFO [2025-11-08 02:07:57] 
Checking sample information
INFO [2025-11-08 02:07:57] Checking 'Injection_order' column in feature data
INFO [2025-11-08 02:07:57] Checking 'Sample_ID' column in pheno data
INFO [2025-11-08 02:07:57] Checking 'QC' column in feature data
INFO [2025-11-08 02:07:57] Checking that feature abundances only contain numeric values
INFO [2025-11-08 02:07:57] 
Checking feature information
INFO [2025-11-08 02:07:57] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-08 02:07:57] Checking that m/z and retention time values are reasonable.
INFO [2025-11-08 02:07:57] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-08 02:07:57] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-08 02:07:57] Checking that feature data includes a 'Split' column
INFO [2025-11-08 02:07:57] Checking that feature data includes a 'Flag' column
INFO [2025-11-08 02:07:57] Detecting corner position
INFO [2025-11-08 02:07:57] Corner detected correctly at row 11, column H
INFO [2025-11-08 02:07:57] 
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-08 02:07:57] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-08 02:07:57] Naming the last column of sample information "rp_pos_Datafile"
INFO [2025-11-08 02:07:57] 
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-08 02:07:57] 
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-08 02:07:57] Pheno data was cleaned
INFO [2025-11-08 02:07:57] Feature data was cleaned
INFO [2025-11-08 02:07:57] 
Checking sample information
INFO [2025-11-08 02:07:57] Checking 'Injection_order' column in feature data
INFO [2025-11-08 02:07:57] Checking 'Sample_ID' column in pheno data
INFO [2025-11-08 02:07:57] Checking 'QC' column in feature data
INFO [2025-11-08 02:07:57] Checking that feature abundances only contain numeric values
INFO [2025-11-08 02:07:57] 
Checking feature information
INFO [2025-11-08 02:07:57] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-08 02:07:57] Checking that m/z and retention time values are reasonable.
INFO [2025-11-08 02:07:57] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-08 02:07:57] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-08 02:07:57] Checking that feature data includes a 'Split' column
INFO [2025-11-08 02:07:57] Checking that feature data includes a 'Flag' column
INFO [2025-11-08 02:07:58] Injection order differs between modes.Creating dummy injection order
INFO [2025-11-08 02:07:58] Dummy injection order (row numbers) created
INFO [2025-11-08 02:07:58] Merging objects with unequal amounts of samples.
INFO [2025-11-08 02:07:58] Samples only in first object:
INFO [2025-11-08 02:07:58] ID_666

INFO [2025-11-08 02:07:58] Samples only in second object:
INFO [2025-11-08 02:07:58] Demo_2

INFO [2025-11-08 02:07:58] Injection order differs between modes.Creating dummy injection order
INFO [2025-11-08 02:07:58] Dummy injection order (row numbers) created
INFO [2025-11-08 02:07:58] Merging objects with unequal amounts of samples.
INFO [2025-11-08 02:07:58] Samples only in first object:
INFO [2025-11-08 02:07:58] ID_666

INFO [2025-11-08 02:07:58] Samples only in second object:
INFO [2025-11-08 02:07:58] 

INFO [2025-11-08 02:07:58] Injection order differs between modes.Creating dummy injection order
INFO [2025-11-08 02:07:58] Dummy injection order (row numbers) created
INFO [2025-11-08 02:07:58] Merging objects with unequal amounts of samples.
INFO [2025-11-08 02:07:58] Samples only in first object:
INFO [2025-11-08 02:07:58] ID_666, Demo_22

INFO [2025-11-08 02:07:58] Samples only in second object:
INFO [2025-11-08 02:07:58] ID_999

INFO [2025-11-08 02:07:58] Starting logging
INFO [2025-11-08 02:07:58] Finished analysis. Sat Nov  8 02:07:58 2025
Session info:

INFO [2025-11-08 02:07:58] R Under development (unstable) (2025-10-20 r88955)
INFO [2025-11-08 02:07:58] Platform: x86_64-pc-linux-gnu
INFO [2025-11-08 02:07:58] Running under: Ubuntu 24.04.3 LTS
INFO [2025-11-08 02:07:58] 
INFO [2025-11-08 02:07:58] Matrix products: default
INFO [2025-11-08 02:07:58] BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so 
INFO [2025-11-08 02:07:58] LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
INFO [2025-11-08 02:07:58] 
INFO [2025-11-08 02:07:58] locale:
INFO [2025-11-08 02:07:58]  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
INFO [2025-11-08 02:07:58]  [3] LC_TIME=en_GB              LC_COLLATE=C              
INFO [2025-11-08 02:07:58]  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
INFO [2025-11-08 02:07:58]  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
INFO [2025-11-08 02:07:58]  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
INFO [2025-11-08 02:07:58] [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
INFO [2025-11-08 02:07:58] 
INFO [2025-11-08 02:07:58] time zone: America/New_York
INFO [2025-11-08 02:07:58] tzcode source: system (glibc)
INFO [2025-11-08 02:07:58] 
INFO [2025-11-08 02:07:58] attached base packages:
INFO [2025-11-08 02:07:58] [1] stats4    stats     graphics  grDevices utils     datasets  methods  
INFO [2025-11-08 02:07:58] [8] base     
INFO [2025-11-08 02:07:58] 
INFO [2025-11-08 02:07:58] other attached packages:
INFO [2025-11-08 02:07:58]  [1] notame_1.1.0                SummarizedExperiment_1.41.0
INFO [2025-11-08 02:07:58]  [3] Biobase_2.71.0              GenomicRanges_1.63.0       
INFO [2025-11-08 02:07:58]  [5] Seqinfo_1.1.0               IRanges_2.45.0             
INFO [2025-11-08 02:07:58]  [7] S4Vectors_0.49.0            BiocGenerics_0.57.0        
INFO [2025-11-08 02:07:58]  [9] generics_0.1.4              MatrixGenerics_1.23.0      
INFO [2025-11-08 02:07:58] [11] matrixStats_1.5.0           ggplot2_4.0.0              
INFO [2025-11-08 02:07:58] [13] testthat_3.2.3             
INFO [2025-11-08 02:07:58] 
INFO [2025-11-08 02:07:58] loaded via a namespace (and not attached):
INFO [2025-11-08 02:07:58]  [1] Matrix_1.7-4         gtable_0.3.6         futile.logger_1.4.3 
INFO [2025-11-08 02:07:58]  [4] dplyr_1.1.4          compiler_4.6.0       brio_1.1.5          
INFO [2025-11-08 02:07:58]  [7] zip_2.3.3            Rcpp_1.1.0           tidyselect_1.2.1    
INFO [2025-11-08 02:07:58] [10] tidyr_1.3.1          scales_1.4.0         lattice_0.22-7      
INFO [2025-11-08 02:07:58] [13] XVector_0.51.0       R6_2.6.1             S4Arrays_1.11.0     
INFO [2025-11-08 02:07:58] [16] openxlsx_4.2.8.1     tibble_3.3.0         DelayedArray_0.37.0 
INFO [2025-11-08 02:07:58] [19] desc_1.4.3           pillar_1.11.1        RColorBrewer_1.1-3  
INFO [2025-11-08 02:07:58] [22] rlang_1.1.6          stringi_1.8.7        S7_0.2.0            
INFO [2025-11-08 02:07:58] [25] viridisLite_0.4.2    SparseArray_1.11.1   cli_3.6.5           
INFO [2025-11-08 02:07:58] [28] formatR_1.14         withr_3.0.2          magrittr_2.0.4      
INFO [2025-11-08 02:07:58] [31] futile.options_1.0.1 grid_4.6.0           lifecycle_1.0.4     
INFO [2025-11-08 02:07:58] [34] waldo_0.6.2          vctrs_0.6.5          glue_1.8.0          
INFO [2025-11-08 02:07:58] [37] lambda.r_1.2.4       farver_2.1.2         abind_1.4-8         
INFO [2025-11-08 02:07:58] [40] purrr_1.2.0          tools_4.6.0          pkgconfig_2.0.3     
INFO [2025-11-08 02:07:58] New line
INFO [2025-11-08 02:07:58] Starting logging
INFO [2025-11-08 02:07:58] New line
INFO [2025-11-08 02:07:58] Finished analysis. Sat Nov  8 02:07:58 2025
Session info:

INFO [2025-11-08 02:07:59] R Under development (unstable) (2025-10-20 r88955)
INFO [2025-11-08 02:07:59] Platform: x86_64-pc-linux-gnu
INFO [2025-11-08 02:07:59] Running under: Ubuntu 24.04.3 LTS
INFO [2025-11-08 02:07:59] 
INFO [2025-11-08 02:07:59] Matrix products: default
INFO [2025-11-08 02:07:59] BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so 
INFO [2025-11-08 02:07:59] LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
INFO [2025-11-08 02:07:59] 
INFO [2025-11-08 02:07:59] locale:
INFO [2025-11-08 02:07:59]  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
INFO [2025-11-08 02:07:59]  [3] LC_TIME=en_GB              LC_COLLATE=C              
INFO [2025-11-08 02:07:59]  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
INFO [2025-11-08 02:07:59]  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
INFO [2025-11-08 02:07:59]  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
INFO [2025-11-08 02:07:59] [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
INFO [2025-11-08 02:07:59] 
INFO [2025-11-08 02:07:59] time zone: America/New_York
INFO [2025-11-08 02:07:59] tzcode source: system (glibc)
INFO [2025-11-08 02:07:59] 
INFO [2025-11-08 02:07:59] attached base packages:
INFO [2025-11-08 02:07:59] [1] stats4    stats     graphics  grDevices utils     datasets  methods  
INFO [2025-11-08 02:07:59] [8] base     
INFO [2025-11-08 02:07:59] 
INFO [2025-11-08 02:07:59] other attached packages:
INFO [2025-11-08 02:07:59]  [1] notame_1.1.0                SummarizedExperiment_1.41.0
INFO [2025-11-08 02:07:59]  [3] Biobase_2.71.0              GenomicRanges_1.63.0       
INFO [2025-11-08 02:07:59]  [5] Seqinfo_1.1.0               IRanges_2.45.0             
INFO [2025-11-08 02:07:59]  [7] S4Vectors_0.49.0            BiocGenerics_0.57.0        
INFO [2025-11-08 02:07:59]  [9] generics_0.1.4              MatrixGenerics_1.23.0      
INFO [2025-11-08 02:07:59] [11] matrixStats_1.5.0           ggplot2_4.0.0              
INFO [2025-11-08 02:07:59] [13] testthat_3.2.3             
INFO [2025-11-08 02:07:59] 
INFO [2025-11-08 02:07:59] loaded via a namespace (and not attached):
INFO [2025-11-08 02:07:59]  [1] Matrix_1.7-4         gtable_0.3.6         futile.logger_1.4.3 
INFO [2025-11-08 02:07:59]  [4] dplyr_1.1.4          compiler_4.6.0       brio_1.1.5          
INFO [2025-11-08 02:07:59]  [7] zip_2.3.3            Rcpp_1.1.0           tidyselect_1.2.1    
INFO [2025-11-08 02:07:59] [10] tidyr_1.3.1          scales_1.4.0         lattice_0.22-7      
INFO [2025-11-08 02:07:59] [13] XVector_0.51.0       R6_2.6.1             S4Arrays_1.11.0     
INFO [2025-11-08 02:07:59] [16] openxlsx_4.2.8.1     tibble_3.3.0         DelayedArray_0.37.0 
INFO [2025-11-08 02:07:59] [19] desc_1.4.3           pillar_1.11.1        RColorBrewer_1.1-3  
INFO [2025-11-08 02:07:59] [22] rlang_1.1.6          stringi_1.8.7        S7_0.2.0            
INFO [2025-11-08 02:07:59] [25] viridisLite_0.4.2    SparseArray_1.11.1   cli_3.6.5           
INFO [2025-11-08 02:07:59] [28] formatR_1.14         withr_3.0.2          magrittr_2.0.4      
INFO [2025-11-08 02:07:59] [31] futile.options_1.0.1 grid_4.6.0           lifecycle_1.0.4     
INFO [2025-11-08 02:07:59] [34] waldo_0.6.2          vctrs_0.6.5          glue_1.8.0          
INFO [2025-11-08 02:07:59] [37] lambda.r_1.2.4       farver_2.1.2         abind_1.4-8         
INFO [2025-11-08 02:07:59] [40] purrr_1.2.0          tools_4.6.0          pkgconfig_2.0.3     
INFO [2025-11-08 02:07:59] New line
INFO [2025-11-08 02:07:59] 
Starting random forest imputation at 2025-11-08 02:07:59.220014
INFO [2025-11-08 02:08:01] Out-of-bag error in random forest imputation: 0.471
INFO [2025-11-08 02:08:01] Random forest imputation finished at 2025-11-08 02:08:01.307179 

INFO [2025-11-08 02:08:01] 
Starting random forest imputation at 2025-11-08 02:08:01.539048
INFO [2025-11-08 02:08:05] Out-of-bag error in random forest imputation: 0.472
INFO [2025-11-08 02:08:05] Random forest imputation finished at 2025-11-08 02:08:05.250542 

INFO [2025-11-08 02:08:05] 
Starting random forest imputation at 2025-11-08 02:08:05.26368
INFO [2025-11-08 02:08:07] Out-of-bag error in random forest imputation: 0.469
INFO [2025-11-08 02:08:07] Random forest imputation finished at 2025-11-08 02:08:07.94239 

INFO [2025-11-08 02:08:07] 
Starting random forest imputation at 2025-11-08 02:08:07.997162
INFO [2025-11-08 02:08:10] Out-of-bag error in random forest imputation: 0.468
INFO [2025-11-08 02:08:10] Random forest imputation finished at 2025-11-08 02:08:10.963229 

INFO [2025-11-08 02:08:11] Starting PQN normalization
INFO [2025-11-08 02:08:11] Using median of qc samples as reference spectrum
INFO [2025-11-08 02:08:11] Starting PQN normalization
INFO [2025-11-08 02:08:11] Using median of all samples as reference spectrum
INFO [2025-11-08 02:08:11] Starting PQN normalization
INFO [2025-11-08 02:08:11] Using mean of qc samples as reference spectrum
INFO [2025-11-08 02:08:11] Starting PQN normalization
INFO [2025-11-08 02:08:11] Using mean of all samples as reference spectrum
INFO [2025-11-08 02:08:11] 
92% of features flagged for low quality
INFO [2025-11-08 02:08:11] Starting PQN normalization
INFO [2025-11-08 02:08:11] Using median of qc samples as reference spectrum
INFO [2025-11-08 02:08:11] Starting drift correction
INFO [2025-11-08 02:08:11] Zero values in feature abundances detected. Zeroes will be replaced with 1.1.
INFO [2025-11-08 02:08:15] Recomputing quality metrics for drift corrected data
INFO [2025-11-08 02:08:15] Drift correction performed
INFO [2025-11-08 02:08:15] Inspecting drift correction results
INFO [2025-11-08 02:08:15] Original quality metrics missing, recomputing
INFO [2025-11-08 02:08:15] 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 
 29.619   3.151  28.257

Example timings

notame.Rcheck/notame-Ex.timings

name	user	system	elapsed
assess_quality	0.168	0.019	0.187
citations	0.259	0.003	0.263
cluster_features	0.207	0.037	0.245
combined_data	0.047	0.035	0.082
compress_clusters	0.122	0.028	0.150
correct_drift	2.935	0.269	3.021
drop_flagged	0.105	0.008	0.114
drop_qcs	0.036	0.002	0.039
finish_log	0.028	0.007	0.036
fix_MSMS	0.088	0.009	0.097
fix_object	0.109	0.030	0.139
flag	0.024	0.005	0.030
flag_contaminants	0.165	0.031	0.196
flag_detection	0.209	0.013	0.223
flag_quality	0.188	0.006	0.194
flag_report	0.294	0.020	0.314
import_from_excel	0.245	0.012	0.258
impute_rf	1.899	0.282	1.583
impute_simple	0.080	0.005	0.087
init_log	0.002	0.001	0.004
inverse_normalize	0.041	0.003	0.044
join_colData	0.028	0.004	0.032
join_rowData	0.021	0.002	0.024
log_text	0.004	0.000	0.005
mark_nas	0.035	0.002	0.037
merge_notame_sets	0.482	0.027	0.508
pca_bhattacharyya_dist	6.552	0.776	7.328
perform_repeatability	0.160	0.004	0.163
pqn_normalization	0.060	0.003	0.063
quality	0.125	0.009	0.134
ruvs_qc	0.151	0.005	0.156
write_to_excel	0.174	0.004	0.178