Vilhelm Suksi
| Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1466/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| notame 0.99.7 (landing page) Vilhelm Suksi
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the notame package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/notame.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: notame |
| Version: 0.99.7 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:notame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings notame_0.99.7.tar.gz |
| StartedAt: 2025-10-17 11:44:02 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 11:49:10 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 308.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: notame.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:notame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings notame_0.99.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/notame.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 8.957 0.522 9.515
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/notame.Rcheck/00check.log’
for details.
notame.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL notame ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/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)
notame.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(notame)
Loading required package: ggplot2
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>
> test_check("notame")
Running tests in parallel requires the 3rd edition
INFO [2025-10-17 11:48:31] Pheno data was cleaned
INFO [2025-10-17 11:48:31] Checking provided sample ID column
INFO [2025-10-17 11:48:31] Column 'Sample_ID' created from id
INFO [2025-10-17 11:48:31] Pheno data was cleaned
INFO [2025-10-17 11:48:31] Sample ID generated from injection orders and prefix ID_
INFO [2025-10-17 11:48:31] Pheno data was cleaned
INFO [2025-10-17 11:48:31] Pheno data was cleaned
INFO [2025-10-17 11:48:31] Adding running index to 'QC' sample IDs
INFO [2025-10-17 11:48:31] Pheno data was cleaned
INFO [2025-10-17 11:48:31] Initializing 'Flag' column with unflagged features
INFO [2025-10-17 11:48:31] Assigning HILIC_pos as the value of the Split column for each feature
INFO [2025-10-17 11:48:31] Feature data was cleaned
INFO [2025-10-17 11:48:31] Initializing 'Flag' column with unflagged features
INFO [2025-10-17 11:48:31] Feature_ID column not found, creating feature IDs
INFO [2025-10-17 11:48:31] Initializing 'Flag' column with unflagged features
INFO [2025-10-17 11:48:31] Feature_ID column not found, creating feature IDs
INFO [2025-10-17 11:48:31] Initializing 'Flag' column with unflagged features
INFO [2025-10-17 11:48:31] Feature_ID column not found, creating feature IDs
INFO [2025-10-17 11:48:31] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-17 11:48:31] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-17 11:48:31] Creating feature IDs from Split, m/z and retention time
INFO [2025-10-17 11:48:31] Feature data was cleaned
INFO [2025-10-17 11:48:31] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:31] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:31] Creating feature IDs from Split, m/z and retention time
INFO [2025-10-17 11:48:31] Corner detected correctly at row 4, column D
INFO [2025-10-17 11:48:31]
Extracting sample information from rows 1 to 4 and columns E to P
INFO [2025-10-17 11:48:31] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-17 11:48:31] Naming the last column of sample information "easy_Datafile"
INFO [2025-10-17 11:48:31]
Extracting feature information from rows 5 to 14 and columns A to D
INFO [2025-10-17 11:48:31]
Extracting feature abundances from rows 5 to 14 and columns E to P
INFO [2025-10-17 11:48:31] Sample ID generated from injection orders and prefix TEST_
INFO [2025-10-17 11:48:31] Pheno data was cleaned
INFO [2025-10-17 11:48:31] Initializing 'Flag' column with unflagged features
INFO [2025-10-17 11:48:31] Assigning easy as the value of the Split column for each feature
INFO [2025-10-17 11:48:31] Feature_ID column not found, creating feature IDs
INFO [2025-10-17 11:48:31] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:32] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:32] Creating feature IDs from Split, m/z and retention time
INFO [2025-10-17 11:48:32] Feature data was cleaned
INFO [2025-10-17 11:48:32]
Checking sample information
INFO [2025-10-17 11:48:32] Checking 'Injection_order' column in feature data
INFO [2025-10-17 11:48:32] Checking 'Sample_ID' column in pheno data
INFO [2025-10-17 11:48:32] Checking 'QC' column in feature data
INFO [2025-10-17 11:48:32] Checking that feature abundances only contain numeric values
INFO [2025-10-17 11:48:32]
Checking feature information
INFO [2025-10-17 11:48:32] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-17 11:48:32] Checking that m/z and retention time values are reasonable.
INFO [2025-10-17 11:48:32] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:32] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:32] Checking that feature data includes a 'Split' column
INFO [2025-10-17 11:48:32] Checking that feature data includes a 'Flag' column
INFO [2025-10-17 11:48:32] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:32] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:32] Creating feature IDs from Split, m/z and retention time
INFO [2025-10-17 11:48:32] Corner detected correctly at row 4, column F
INFO [2025-10-17 11:48:32]
Extracting sample information from rows 1 to 4 and columns G to R
INFO [2025-10-17 11:48:32] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-17 11:48:32] Naming the last column of sample information "Datafile"
INFO [2025-10-17 11:48:32]
Extracting feature information from rows 5 to 20 and columns A to F
INFO [2025-10-17 11:48:32]
Extracting feature abundances from rows 5 to 20 and columns G to R
INFO [2025-10-17 11:48:32] Sample ID generated from injection orders and prefix TEST_
INFO [2025-10-17 11:48:32] Pheno data was cleaned
INFO [2025-10-17 11:48:32] Initializing 'Flag' column with unflagged features
INFO [2025-10-17 11:48:32] Creating Split column from Column, Mode
INFO [2025-10-17 11:48:32] Feature_ID column not found, creating feature IDs
INFO [2025-10-17 11:48:32] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:32] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:32] Creating feature IDs from Split, m/z and retention time
INFO [2025-10-17 11:48:32] Feature data was cleaned
INFO [2025-10-17 11:48:32]
Checking sample information
INFO [2025-10-17 11:48:32] Checking 'Injection_order' column in feature data
INFO [2025-10-17 11:48:32] Checking 'Sample_ID' column in pheno data
INFO [2025-10-17 11:48:32] Checking 'QC' column in feature data
INFO [2025-10-17 11:48:32] Checking that feature abundances only contain numeric values
INFO [2025-10-17 11:48:32]
Checking feature information
INFO [2025-10-17 11:48:32] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-17 11:48:32] Checking that m/z and retention time values are reasonable.
INFO [2025-10-17 11:48:32] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:32] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-10-17 11:48:32] Checking that feature data includes a 'Split' column
INFO [2025-10-17 11:48:32] Checking that feature data includes a 'Flag' column
INFO [2025-10-17 11:48:32] Pheno data was cleaned
INFO [2025-10-17 11:48:32] Feature data was cleaned
INFO [2025-10-17 11:48:32] Pheno data was cleaned
INFO [2025-10-17 11:48:32] Feature data was cleaned
INFO [2025-10-17 11:48:33] Detecting corner position
INFO [2025-10-17 11:48:33] Corner detected correctly at row 11, column H
INFO [2025-10-17 11:48:33]
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-10-17 11:48:33] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-17 11:48:33] Naming the last column of sample information "hilic_neg_Datafile"
INFO [2025-10-17 11:48:33]
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-10-17 11:48:33]
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-10-17 11:48:33] Pheno data was cleaned
INFO [2025-10-17 11:48:33] Feature data was cleaned
INFO [2025-10-17 11:48:33]
Checking sample information
INFO [2025-10-17 11:48:33] Checking 'Injection_order' column in feature data
INFO [2025-10-17 11:48:33] Checking 'Sample_ID' column in pheno data
INFO [2025-10-17 11:48:33] Checking 'QC' column in feature data
INFO [2025-10-17 11:48:33] Checking that feature abundances only contain numeric values
INFO [2025-10-17 11:48:33]
Checking feature information
INFO [2025-10-17 11:48:33] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-17 11:48:33] Checking that m/z and retention time values are reasonable.
INFO [2025-10-17 11:48:33] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-17 11:48:33] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-17 11:48:33] Checking that feature data includes a 'Split' column
INFO [2025-10-17 11:48:33] Checking that feature data includes a 'Flag' column
INFO [2025-10-17 11:48:33] Detecting corner position
INFO [2025-10-17 11:48:33] Corner detected correctly at row 11, column H
INFO [2025-10-17 11:48:33]
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-10-17 11:48:33] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-17 11:48:33] Naming the last column of sample information "hilic_pos_Datafile"
INFO [2025-10-17 11:48:33]
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-10-17 11:48:33]
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-10-17 11:48:33] Pheno data was cleaned
INFO [2025-10-17 11:48:33] Feature data was cleaned
INFO [2025-10-17 11:48:33]
Checking sample information
INFO [2025-10-17 11:48:33] Checking 'Injection_order' column in feature data
INFO [2025-10-17 11:48:33] Checking 'Sample_ID' column in pheno data
INFO [2025-10-17 11:48:33] Checking 'QC' column in feature data
INFO [2025-10-17 11:48:33] Checking that feature abundances only contain numeric values
INFO [2025-10-17 11:48:33]
Checking feature information
INFO [2025-10-17 11:48:33] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-17 11:48:33] Checking that m/z and retention time values are reasonable.
INFO [2025-10-17 11:48:33] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-17 11:48:33] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-17 11:48:33] Checking that feature data includes a 'Split' column
INFO [2025-10-17 11:48:33] Checking that feature data includes a 'Flag' column
INFO [2025-10-17 11:48:33] Detecting corner position
INFO [2025-10-17 11:48:33] Corner detected correctly at row 11, column H
INFO [2025-10-17 11:48:33]
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-10-17 11:48:33] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-17 11:48:33] Naming the last column of sample information "rp_neg_Datafile"
INFO [2025-10-17 11:48:33]
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-10-17 11:48:33]
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-10-17 11:48:33] Pheno data was cleaned
INFO [2025-10-17 11:48:33] Feature data was cleaned
INFO [2025-10-17 11:48:33]
Checking sample information
INFO [2025-10-17 11:48:33] Checking 'Injection_order' column in feature data
INFO [2025-10-17 11:48:33] Checking 'Sample_ID' column in pheno data
INFO [2025-10-17 11:48:33] Checking 'QC' column in feature data
INFO [2025-10-17 11:48:33] Checking that feature abundances only contain numeric values
INFO [2025-10-17 11:48:33]
Checking feature information
INFO [2025-10-17 11:48:33] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-17 11:48:33] Checking that m/z and retention time values are reasonable.
INFO [2025-10-17 11:48:33] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-17 11:48:33] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-17 11:48:33] Checking that feature data includes a 'Split' column
INFO [2025-10-17 11:48:33] Checking that feature data includes a 'Flag' column
INFO [2025-10-17 11:48:33] Detecting corner position
INFO [2025-10-17 11:48:33] Corner detected correctly at row 11, column H
INFO [2025-10-17 11:48:33]
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-10-17 11:48:33] Replacing spaces in sample information column names with underscores (_)
INFO [2025-10-17 11:48:33] Naming the last column of sample information "rp_pos_Datafile"
INFO [2025-10-17 11:48:33]
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-10-17 11:48:33]
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-10-17 11:48:33] Pheno data was cleaned
INFO [2025-10-17 11:48:33] Feature data was cleaned
INFO [2025-10-17 11:48:33]
Checking sample information
INFO [2025-10-17 11:48:33] Checking 'Injection_order' column in feature data
INFO [2025-10-17 11:48:33] Checking 'Sample_ID' column in pheno data
INFO [2025-10-17 11:48:33] Checking 'QC' column in feature data
INFO [2025-10-17 11:48:33] Checking that feature abundances only contain numeric values
INFO [2025-10-17 11:48:33]
Checking feature information
INFO [2025-10-17 11:48:33] Checking that feature IDs are unique and not storedas numbers
INFO [2025-10-17 11:48:33] Checking that m/z and retention time values are reasonable.
INFO [2025-10-17 11:48:33] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-17 11:48:33] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-17 11:48:33] Checking that feature data includes a 'Split' column
INFO [2025-10-17 11:48:33] Checking that feature data includes a 'Flag' column
INFO [2025-10-17 11:48:34] Injection order differs between modes.Creating dummy injection order
INFO [2025-10-17 11:48:34] Dummy injection order (row numbers) created
INFO [2025-10-17 11:48:34] Merging objects with unequal amounts of samples.
INFO [2025-10-17 11:48:34] Samples only in first object:
INFO [2025-10-17 11:48:34] ID_666
INFO [2025-10-17 11:48:34] Samples only in second object:
INFO [2025-10-17 11:48:34] Demo_2
INFO [2025-10-17 11:48:34] Injection order differs between modes.Creating dummy injection order
INFO [2025-10-17 11:48:34] Dummy injection order (row numbers) created
INFO [2025-10-17 11:48:34] Merging objects with unequal amounts of samples.
INFO [2025-10-17 11:48:34] Samples only in first object:
INFO [2025-10-17 11:48:34] ID_666
INFO [2025-10-17 11:48:34] Samples only in second object:
INFO [2025-10-17 11:48:34]
INFO [2025-10-17 11:48:34] Injection order differs between modes.Creating dummy injection order
INFO [2025-10-17 11:48:34] Dummy injection order (row numbers) created
INFO [2025-10-17 11:48:34] Merging objects with unequal amounts of samples.
INFO [2025-10-17 11:48:34] Samples only in first object:
INFO [2025-10-17 11:48:34] ID_666, Demo_22
INFO [2025-10-17 11:48:34] Samples only in second object:
INFO [2025-10-17 11:48:34] ID_999
INFO [2025-10-17 11:48:35] Starting logging
INFO [2025-10-17 11:48:35] Finished analysis. Fri Oct 17 11:48:35 2025
Session info:
INFO [2025-10-17 11:48:35] R version 4.5.0 (2025-04-11)
INFO [2025-10-17 11:48:35] Platform: aarch64-unknown-linux-gnu
INFO [2025-10-17 11:48:35] Running under: openEuler 24.03 (LTS)
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] Matrix products: default
INFO [2025-10-17 11:48:35] BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.25.so; LAPACK version 3.11.0
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] locale:
INFO [2025-10-17 11:48:35] [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
INFO [2025-10-17 11:48:35] [3] LC_TIME=en_GB LC_COLLATE=C
INFO [2025-10-17 11:48:35] [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
INFO [2025-10-17 11:48:35] [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
INFO [2025-10-17 11:48:35] [9] LC_ADDRESS=C LC_TELEPHONE=C
INFO [2025-10-17 11:48:35] [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] time zone: UTC
INFO [2025-10-17 11:48:35] tzcode source: system (glibc)
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] attached base packages:
INFO [2025-10-17 11:48:35] [1] stats4 stats graphics grDevices utils datasets methods
INFO [2025-10-17 11:48:35] [8] base
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] other attached packages:
INFO [2025-10-17 11:48:35] [1] notame_0.99.7 SummarizedExperiment_1.39.2
INFO [2025-10-17 11:48:35] [3] Biobase_2.69.1 GenomicRanges_1.61.5
INFO [2025-10-17 11:48:35] [5] Seqinfo_0.99.2 IRanges_2.43.5
INFO [2025-10-17 11:48:35] [7] S4Vectors_0.47.4 BiocGenerics_0.55.3
INFO [2025-10-17 11:48:35] [9] generics_0.1.4 MatrixGenerics_1.21.0
INFO [2025-10-17 11:48:35] [11] matrixStats_1.5.0 ggplot2_4.0.0
INFO [2025-10-17 11:48:35] [13] testthat_3.2.3
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] loaded via a namespace (and not attached):
INFO [2025-10-17 11:48:35] [1] Matrix_1.7-4 gtable_0.3.6 futile.logger_1.4.3
INFO [2025-10-17 11:48:35] [4] dplyr_1.1.4 compiler_4.5.0 crayon_1.5.3
INFO [2025-10-17 11:48:35] [7] brio_1.1.5 zip_2.3.3 Rcpp_1.1.0
INFO [2025-10-17 11:48:35] [10] tidyselect_1.2.1 tidyr_1.3.1 scales_1.4.0
INFO [2025-10-17 11:48:35] [13] lattice_0.22-7 R6_2.6.1 XVector_0.49.1
INFO [2025-10-17 11:48:35] [16] S4Arrays_1.9.1 openxlsx_4.2.8 DelayedArray_0.35.3
INFO [2025-10-17 11:48:35] [19] tibble_3.3.0 desc_1.4.3 pillar_1.11.1
INFO [2025-10-17 11:48:35] [22] RColorBrewer_1.1-3 rlang_1.1.6 stringi_1.8.7
INFO [2025-10-17 11:48:35] [25] S7_0.2.0 viridisLite_0.4.2 SparseArray_1.9.1
INFO [2025-10-17 11:48:35] [28] cli_3.6.5 formatR_1.14 withr_3.0.2
INFO [2025-10-17 11:48:35] [31] magrittr_2.0.4 futile.options_1.0.1 grid_4.5.0
INFO [2025-10-17 11:48:35] [34] lifecycle_1.0.4 waldo_0.6.2 vctrs_0.6.5
INFO [2025-10-17 11:48:35] [37] glue_1.8.0 lambda.r_1.2.4 farver_2.1.2
INFO [2025-10-17 11:48:35] [40] abind_1.4-8 purrr_1.1.0 tools_4.5.0
INFO [2025-10-17 11:48:35] [43] pkgconfig_2.0.3
INFO [2025-10-17 11:48:35] New line
INFO [2025-10-17 11:48:35] Starting logging
INFO [2025-10-17 11:48:35] New line
INFO [2025-10-17 11:48:35] Finished analysis. Fri Oct 17 11:48:35 2025
Session info:
INFO [2025-10-17 11:48:35] R version 4.5.0 (2025-04-11)
INFO [2025-10-17 11:48:35] Platform: aarch64-unknown-linux-gnu
INFO [2025-10-17 11:48:35] Running under: openEuler 24.03 (LTS)
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] Matrix products: default
INFO [2025-10-17 11:48:35] BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.25.so; LAPACK version 3.11.0
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] locale:
INFO [2025-10-17 11:48:35] [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
INFO [2025-10-17 11:48:35] [3] LC_TIME=en_GB LC_COLLATE=C
INFO [2025-10-17 11:48:35] [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
INFO [2025-10-17 11:48:35] [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
INFO [2025-10-17 11:48:35] [9] LC_ADDRESS=C LC_TELEPHONE=C
INFO [2025-10-17 11:48:35] [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] time zone: UTC
INFO [2025-10-17 11:48:35] tzcode source: system (glibc)
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] attached base packages:
INFO [2025-10-17 11:48:35] [1] stats4 stats graphics grDevices utils datasets methods
INFO [2025-10-17 11:48:35] [8] base
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] other attached packages:
INFO [2025-10-17 11:48:35] [1] notame_0.99.7 SummarizedExperiment_1.39.2
INFO [2025-10-17 11:48:35] [3] Biobase_2.69.1 GenomicRanges_1.61.5
INFO [2025-10-17 11:48:35] [5] Seqinfo_0.99.2 IRanges_2.43.5
INFO [2025-10-17 11:48:35] [7] S4Vectors_0.47.4 BiocGenerics_0.55.3
INFO [2025-10-17 11:48:35] [9] generics_0.1.4 MatrixGenerics_1.21.0
INFO [2025-10-17 11:48:35] [11] matrixStats_1.5.0 ggplot2_4.0.0
INFO [2025-10-17 11:48:35] [13] testthat_3.2.3
INFO [2025-10-17 11:48:35]
INFO [2025-10-17 11:48:35] loaded via a namespace (and not attached):
INFO [2025-10-17 11:48:35] [1] Matrix_1.7-4 gtable_0.3.6 futile.logger_1.4.3
INFO [2025-10-17 11:48:35] [4] dplyr_1.1.4 compiler_4.5.0 crayon_1.5.3
INFO [2025-10-17 11:48:35] [7] brio_1.1.5 zip_2.3.3 Rcpp_1.1.0
INFO [2025-10-17 11:48:35] [10] tidyselect_1.2.1 tidyr_1.3.1 scales_1.4.0
INFO [2025-10-17 11:48:35] [13] lattice_0.22-7 R6_2.6.1 XVector_0.49.1
INFO [2025-10-17 11:48:35] [16] S4Arrays_1.9.1 openxlsx_4.2.8 DelayedArray_0.35.3
INFO [2025-10-17 11:48:35] [19] tibble_3.3.0 desc_1.4.3 pillar_1.11.1
INFO [2025-10-17 11:48:35] [22] RColorBrewer_1.1-3 rlang_1.1.6 stringi_1.8.7
INFO [2025-10-17 11:48:35] [25] S7_0.2.0 viridisLite_0.4.2 SparseArray_1.9.1
INFO [2025-10-17 11:48:35] [28] cli_3.6.5 formatR_1.14 withr_3.0.2
INFO [2025-10-17 11:48:35] [31] magrittr_2.0.4 futile.options_1.0.1 grid_4.5.0
INFO [2025-10-17 11:48:35] [34] lifecycle_1.0.4 waldo_0.6.2 vctrs_0.6.5
INFO [2025-10-17 11:48:35] [37] glue_1.8.0 lambda.r_1.2.4 farver_2.1.2
INFO [2025-10-17 11:48:35] [40] abind_1.4-8 purrr_1.1.0 tools_4.5.0
INFO [2025-10-17 11:48:35] [43] pkgconfig_2.0.3
INFO [2025-10-17 11:48:35] New line
INFO [2025-10-17 11:48:35]
Starting random forest imputation at 2025-10-17 11:48:35.811342
INFO [2025-10-17 11:48:44] Out-of-bag error in random forest imputation: 0.47
INFO [2025-10-17 11:48:44] Random forest imputation finished at 2025-10-17 11:48:44.845694
INFO [2025-10-17 11:48:45]
Starting random forest imputation at 2025-10-17 11:48:45.195845
INFO [2025-10-17 11:48:51] Out-of-bag error in random forest imputation: 0.47
INFO [2025-10-17 11:48:51] Random forest imputation finished at 2025-10-17 11:48:51.877673
INFO [2025-10-17 11:48:51]
Starting random forest imputation at 2025-10-17 11:48:51.897233
INFO [2025-10-17 11:48:56] Out-of-bag error in random forest imputation: 0.47
INFO [2025-10-17 11:48:56] Random forest imputation finished at 2025-10-17 11:48:56.084601
INFO [2025-10-17 11:48:56]
Starting random forest imputation at 2025-10-17 11:48:56.148282
INFO [2025-10-17 11:49:01] Out-of-bag error in random forest imputation: 0.469
INFO [2025-10-17 11:49:01] Random forest imputation finished at 2025-10-17 11:49:01.766273
INFO [2025-10-17 11:49:02] Starting PQN normalization
INFO [2025-10-17 11:49:02] Using median of qc samples as reference spectrum
INFO [2025-10-17 11:49:02] Starting PQN normalization
INFO [2025-10-17 11:49:02] Using median of all samples as reference spectrum
INFO [2025-10-17 11:49:02] Starting PQN normalization
INFO [2025-10-17 11:49:02] Using mean of qc samples as reference spectrum
INFO [2025-10-17 11:49:02] Starting PQN normalization
INFO [2025-10-17 11:49:02] Using mean of all samples as reference spectrum
INFO [2025-10-17 11:49:02]
92% of features flagged for low quality
INFO [2025-10-17 11:49:02] Starting PQN normalization
INFO [2025-10-17 11:49:02] Using median of qc samples as reference spectrum
INFO [2025-10-17 11:49:02] Starting drift correction
INFO [2025-10-17 11:49:02] Zero values in feature abundances detected. Zeroes will be replaced with 1.1.
INFO [2025-10-17 11:49:05] Recomputing quality metrics for drift corrected data
INFO [2025-10-17 11:49:06] Drift correction performed
INFO [2025-10-17 11:49:06] Inspecting drift correction results
INFO [2025-10-17 11:49:06] Original quality metrics missing, recomputing
INFO [2025-10-17 11:49:06] 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
45.049 1.285 46.389
notame.Rcheck/notame-Ex.timings
| name | user | system | elapsed | |
| assess_quality | 0.229 | 0.016 | 0.246 | |
| citations | 0.383 | 0.004 | 0.388 | |
| cluster_features | 0.301 | 0.048 | 0.352 | |
| combined_data | 0.064 | 0.008 | 0.072 | |
| compress_clusters | 0.204 | 0.024 | 0.228 | |
| correct_drift | 2.933 | 0.314 | 3.055 | |
| drop_flagged | 0.151 | 0.012 | 0.164 | |
| drop_qcs | 0.040 | 0.011 | 0.051 | |
| finish_log | 0.043 | 0.006 | 0.068 | |
| fix_MSMS | 0.140 | 0.012 | 0.153 | |
| fix_object | 0.203 | 0.000 | 0.204 | |
| flag | 0.032 | 0.008 | 0.040 | |
| flag_contaminants | 0.275 | 0.008 | 0.283 | |
| flag_detection | 0.333 | 0.000 | 0.334 | |
| flag_quality | 0.335 | 0.000 | 0.336 | |
| flag_report | 0.454 | 0.004 | 0.460 | |
| import_from_excel | 0.364 | 0.036 | 0.406 | |
| impute_rf | 4.307 | 0.032 | 4.351 | |
| impute_simple | 0.176 | 0.008 | 0.184 | |
| init_log | 0.004 | 0.000 | 0.004 | |
| inverse_normalize | 0.050 | 0.012 | 0.062 | |
| join_colData | 0.046 | 0.000 | 0.046 | |
| join_rowData | 0.033 | 0.000 | 0.032 | |
| log_text | 0.002 | 0.004 | 0.006 | |
| mark_nas | 0.055 | 0.000 | 0.054 | |
| merge_notame_sets | 0.760 | 0.016 | 0.779 | |
| pca_bhattacharyya_dist | 8.957 | 0.522 | 9.515 | |
| perform_repeatability | 0.263 | 0.000 | 0.263 | |
| pqn_normalization | 0.088 | 0.000 | 0.089 | |
| quality | 0.124 | 0.000 | 0.125 | |
| ruvs_qc | 0.254 | 0.004 | 0.258 | |
| write_to_excel | 0.246 | 0.016 | 0.262 | |