Vilhelm Suksi
| Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 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) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-19 10:13 -0500 (Wed, 19 Nov 2025).
| 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" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| 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 1453/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| notame 1.1.0 (landing page) Vilhelm Suksi
| nebbiolo1 | 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 | | ||||||||
|
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. |
| 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: 2025-11-18 22:47:43 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 22:52:11 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 267.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: notame.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 7.57 0.824 8.453
* 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.
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)
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 [2025-11-18 22:51:41] Pheno data was cleaned
INFO [2025-11-18 22:51:41] Checking provided sample ID column
INFO [2025-11-18 22:51:41] Column 'Sample_ID' created from id
INFO [2025-11-18 22:51:41] Pheno data was cleaned
INFO [2025-11-18 22:51:41] Sample ID generated from injection orders and prefix ID_
INFO [2025-11-18 22:51:41] Pheno data was cleaned
INFO [2025-11-18 22:51:42] Pheno data was cleaned
INFO [2025-11-18 22:51:42] Adding running index to 'QC' sample IDs
INFO [2025-11-18 22:51:42] Pheno data was cleaned
INFO [2025-11-18 22:51:42] Initializing 'Flag' column with unflagged features
INFO [2025-11-18 22:51:42] Assigning HILIC_pos as the value of the Split column for each feature
INFO [2025-11-18 22:51:42] Feature data was cleaned
INFO [2025-11-18 22:51:42] Initializing 'Flag' column with unflagged features
INFO [2025-11-18 22:51:42] Feature_ID column not found, creating feature IDs
INFO [2025-11-18 22:51:42] Initializing 'Flag' column with unflagged features
INFO [2025-11-18 22:51:42] Feature_ID column not found, creating feature IDs
INFO [2025-11-18 22:51:42] Initializing 'Flag' column with unflagged features
INFO [2025-11-18 22:51:42] Feature_ID column not found, creating feature IDs
INFO [2025-11-18 22:51:42] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-18 22:51:42] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-18 22:51:42] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-18 22:51:42] Feature data was cleaned
INFO [2025-11-18 22:51:42] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:42] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:42] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-18 22:51:42] Corner detected correctly at row 4, column D
INFO [2025-11-18 22:51:42]
Extracting sample information from rows 1 to 4 and columns E to P
INFO [2025-11-18 22:51:42] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-18 22:51:42] Naming the last column of sample information "easy_Datafile"
INFO [2025-11-18 22:51:42]
Extracting feature information from rows 5 to 14 and columns A to D
INFO [2025-11-18 22:51:42]
Extracting feature abundances from rows 5 to 14 and columns E to P
INFO [2025-11-18 22:51:42] Sample ID generated from injection orders and prefix TEST_
INFO [2025-11-18 22:51:42] Pheno data was cleaned
INFO [2025-11-18 22:51:42] Initializing 'Flag' column with unflagged features
INFO [2025-11-18 22:51:42] Assigning easy as the value of the Split column for each feature
INFO [2025-11-18 22:51:42] Feature_ID column not found, creating feature IDs
INFO [2025-11-18 22:51:42] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:42] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:42] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-18 22:51:42] Feature data was cleaned
INFO [2025-11-18 22:51:42]
Checking sample information
INFO [2025-11-18 22:51:42] Checking 'Injection_order' column in feature data
INFO [2025-11-18 22:51:42] Checking 'Sample_ID' column in pheno data
INFO [2025-11-18 22:51:42] Checking 'QC' column in feature data
INFO [2025-11-18 22:51:42] Checking that feature abundances only contain numeric values
INFO [2025-11-18 22:51:42]
Checking feature information
INFO [2025-11-18 22:51:42] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-18 22:51:42] Checking that m/z and retention time values are reasonable.
INFO [2025-11-18 22:51:42] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:42] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:42] Checking that feature data includes a 'Split' column
INFO [2025-11-18 22:51:42] Checking that feature data includes a 'Flag' column
INFO [2025-11-18 22:51:42] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:42] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:42] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-18 22:51:42] Corner detected correctly at row 4, column F
INFO [2025-11-18 22:51:42]
Extracting sample information from rows 1 to 4 and columns G to R
INFO [2025-11-18 22:51:42] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-18 22:51:42] Naming the last column of sample information "Datafile"
INFO [2025-11-18 22:51:42]
Extracting feature information from rows 5 to 20 and columns A to F
INFO [2025-11-18 22:51:42]
Extracting feature abundances from rows 5 to 20 and columns G to R
INFO [2025-11-18 22:51:42] Sample ID generated from injection orders and prefix TEST_
INFO [2025-11-18 22:51:42] Pheno data was cleaned
INFO [2025-11-18 22:51:42] Initializing 'Flag' column with unflagged features
INFO [2025-11-18 22:51:42] Creating Split column from Column, Mode
INFO [2025-11-18 22:51:42] Feature_ID column not found, creating feature IDs
INFO [2025-11-18 22:51:42] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:42] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:42] Creating feature IDs from Split, m/z and retention time
INFO [2025-11-18 22:51:42] Feature data was cleaned
INFO [2025-11-18 22:51:42]
Checking sample information
INFO [2025-11-18 22:51:42] Checking 'Injection_order' column in feature data
INFO [2025-11-18 22:51:42] Checking 'Sample_ID' column in pheno data
INFO [2025-11-18 22:51:42] Checking 'QC' column in feature data
INFO [2025-11-18 22:51:43] Checking that feature abundances only contain numeric values
INFO [2025-11-18 22:51:43]
Checking feature information
INFO [2025-11-18 22:51:43] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-18 22:51:43] Checking that m/z and retention time values are reasonable.
INFO [2025-11-18 22:51:43] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:43] Identified m/z column Mass and retention time column RetentionTime
INFO [2025-11-18 22:51:43] Checking that feature data includes a 'Split' column
INFO [2025-11-18 22:51:43] Checking that feature data includes a 'Flag' column
INFO [2025-11-18 22:51:43] Pheno data was cleaned
INFO [2025-11-18 22:51:43] Feature data was cleaned
INFO [2025-11-18 22:51:43] Pheno data was cleaned
INFO [2025-11-18 22:51:43] Feature data was cleaned
INFO [2025-11-18 22:51:43] Detecting corner position
INFO [2025-11-18 22:51:43] Corner detected correctly at row 11, column H
INFO [2025-11-18 22:51:43]
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-18 22:51:43] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-18 22:51:43] Naming the last column of sample information "hilic_neg_Datafile"
INFO [2025-11-18 22:51:43]
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-18 22:51:43]
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-18 22:51:43] Pheno data was cleaned
INFO [2025-11-18 22:51:43] Feature data was cleaned
INFO [2025-11-18 22:51:43]
Checking sample information
INFO [2025-11-18 22:51:43] Checking 'Injection_order' column in feature data
INFO [2025-11-18 22:51:43] Checking 'Sample_ID' column in pheno data
INFO [2025-11-18 22:51:43] Checking 'QC' column in feature data
INFO [2025-11-18 22:51:43] Checking that feature abundances only contain numeric values
INFO [2025-11-18 22:51:43]
Checking feature information
INFO [2025-11-18 22:51:43] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-18 22:51:43] Checking that m/z and retention time values are reasonable.
INFO [2025-11-18 22:51:43] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-18 22:51:43] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-18 22:51:43] Checking that feature data includes a 'Split' column
INFO [2025-11-18 22:51:43] Checking that feature data includes a 'Flag' column
INFO [2025-11-18 22:51:43] Detecting corner position
INFO [2025-11-18 22:51:43] Corner detected correctly at row 11, column H
INFO [2025-11-18 22:51:43]
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-18 22:51:43] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-18 22:51:43] Naming the last column of sample information "hilic_pos_Datafile"
INFO [2025-11-18 22:51:43]
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-18 22:51:43]
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-18 22:51:43] Pheno data was cleaned
INFO [2025-11-18 22:51:43] Feature data was cleaned
INFO [2025-11-18 22:51:43]
Checking sample information
INFO [2025-11-18 22:51:43] Checking 'Injection_order' column in feature data
INFO [2025-11-18 22:51:43] Checking 'Sample_ID' column in pheno data
INFO [2025-11-18 22:51:43] Checking 'QC' column in feature data
INFO [2025-11-18 22:51:43] Checking that feature abundances only contain numeric values
INFO [2025-11-18 22:51:43]
Checking feature information
INFO [2025-11-18 22:51:43] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-18 22:51:43] Checking that m/z and retention time values are reasonable.
INFO [2025-11-18 22:51:43] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-18 22:51:43] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-18 22:51:43] Checking that feature data includes a 'Split' column
INFO [2025-11-18 22:51:43] Checking that feature data includes a 'Flag' column
INFO [2025-11-18 22:51:43] Detecting corner position
INFO [2025-11-18 22:51:43] Corner detected correctly at row 11, column H
INFO [2025-11-18 22:51:43]
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-18 22:51:43] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-18 22:51:43] Naming the last column of sample information "rp_neg_Datafile"
INFO [2025-11-18 22:51:43]
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-18 22:51:43]
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-18 22:51:43] Pheno data was cleaned
INFO [2025-11-18 22:51:43] Feature data was cleaned
INFO [2025-11-18 22:51:43]
Checking sample information
INFO [2025-11-18 22:51:43] Checking 'Injection_order' column in feature data
INFO [2025-11-18 22:51:43] Checking 'Sample_ID' column in pheno data
INFO [2025-11-18 22:51:43] Checking 'QC' column in feature data
INFO [2025-11-18 22:51:43] Checking that feature abundances only contain numeric values
INFO [2025-11-18 22:51:43]
Checking feature information
INFO [2025-11-18 22:51:43] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-18 22:51:43] Checking that m/z and retention time values are reasonable.
INFO [2025-11-18 22:51:43] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-18 22:51:43] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-18 22:51:43] Checking that feature data includes a 'Split' column
INFO [2025-11-18 22:51:43] Checking that feature data includes a 'Flag' column
INFO [2025-11-18 22:51:44] Detecting corner position
INFO [2025-11-18 22:51:44] Corner detected correctly at row 11, column H
INFO [2025-11-18 22:51:44]
Extracting sample information from rows 1 to 11 and columns I to BF
INFO [2025-11-18 22:51:44] Replacing spaces in sample information column names with underscores (_)
INFO [2025-11-18 22:51:44] Naming the last column of sample information "rp_pos_Datafile"
INFO [2025-11-18 22:51:44]
Extracting feature information from rows 12 to 31 and columns A to H
INFO [2025-11-18 22:51:44]
Extracting feature abundances from rows 12 to 31 and columns I to BF
INFO [2025-11-18 22:51:44] Pheno data was cleaned
INFO [2025-11-18 22:51:44] Feature data was cleaned
INFO [2025-11-18 22:51:44]
Checking sample information
INFO [2025-11-18 22:51:44] Checking 'Injection_order' column in feature data
INFO [2025-11-18 22:51:44] Checking 'Sample_ID' column in pheno data
INFO [2025-11-18 22:51:44] Checking 'QC' column in feature data
INFO [2025-11-18 22:51:44] Checking that feature abundances only contain numeric values
INFO [2025-11-18 22:51:44]
Checking feature information
INFO [2025-11-18 22:51:44] Checking that feature IDs are unique and not storedas numbers
INFO [2025-11-18 22:51:44] Checking that m/z and retention time values are reasonable.
INFO [2025-11-18 22:51:44] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-18 22:51:44] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-18 22:51:44] Checking that feature data includes a 'Split' column
INFO [2025-11-18 22:51:44] Checking that feature data includes a 'Flag' column
INFO [2025-11-18 22:51:44] Injection order differs between modes.Creating dummy injection order
INFO [2025-11-18 22:51:44] Dummy injection order (row numbers) created
INFO [2025-11-18 22:51:44] Merging objects with unequal amounts of samples.
INFO [2025-11-18 22:51:44] Samples only in first object:
INFO [2025-11-18 22:51:44] ID_666
INFO [2025-11-18 22:51:44] Samples only in second object:
INFO [2025-11-18 22:51:44] Demo_2
INFO [2025-11-18 22:51:44] Injection order differs between modes.Creating dummy injection order
INFO [2025-11-18 22:51:44] Dummy injection order (row numbers) created
INFO [2025-11-18 22:51:44] Merging objects with unequal amounts of samples.
INFO [2025-11-18 22:51:44] Samples only in first object:
INFO [2025-11-18 22:51:44] ID_666
INFO [2025-11-18 22:51:44] Samples only in second object:
INFO [2025-11-18 22:51:44]
INFO [2025-11-18 22:51:45] Injection order differs between modes.Creating dummy injection order
INFO [2025-11-18 22:51:45] Dummy injection order (row numbers) created
INFO [2025-11-18 22:51:45] Merging objects with unequal amounts of samples.
INFO [2025-11-18 22:51:45] Samples only in first object:
INFO [2025-11-18 22:51:45] ID_666, Demo_22
INFO [2025-11-18 22:51:45] Samples only in second object:
INFO [2025-11-18 22:51:45] ID_999
INFO [2025-11-18 22:51:45] Starting logging
INFO [2025-11-18 22:51:45] Finished analysis. Tue Nov 18 22:51:45 2025
Session info:
INFO [2025-11-18 22:51:45] R Under development (unstable) (2025-10-21 r88958)
INFO [2025-11-18 22:51:45] Platform: x86_64-apple-darwin20
INFO [2025-11-18 22:51:45] Running under: macOS Ventura 13.7.8
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] Matrix products: default
INFO [2025-11-18 22:51:45] BLAS: /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libRblas.0.dylib
INFO [2025-11-18 22:51:45] LAPACK: /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] locale:
INFO [2025-11-18 22:51:45] [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] time zone: America/New_York
INFO [2025-11-18 22:51:45] tzcode source: internal
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] attached base packages:
INFO [2025-11-18 22:51:45] [1] stats4 stats graphics grDevices utils datasets methods
INFO [2025-11-18 22:51:45] [8] base
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] other attached packages:
INFO [2025-11-18 22:51:45] [1] notame_1.1.0 SummarizedExperiment_1.41.0
INFO [2025-11-18 22:51:45] [3] Biobase_2.71.0 GenomicRanges_1.63.0
INFO [2025-11-18 22:51:45] [5] Seqinfo_1.1.0 IRanges_2.45.0
INFO [2025-11-18 22:51:45] [7] S4Vectors_0.49.0 BiocGenerics_0.57.0
INFO [2025-11-18 22:51:45] [9] generics_0.1.4 MatrixGenerics_1.23.0
INFO [2025-11-18 22:51:45] [11] matrixStats_1.5.0 ggplot2_4.0.1
INFO [2025-11-18 22:51:45] [13] testthat_3.3.0
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] loaded via a namespace (and not attached):
INFO [2025-11-18 22:51:45] [1] tidyr_1.3.1 futile.options_1.0.1 SparseArray_1.11.2
INFO [2025-11-18 22:51:45] [4] stringi_1.8.7 lattice_0.22-7 magrittr_2.0.4
INFO [2025-11-18 22:51:45] [7] grid_4.6.0 RColorBrewer_1.1-3 Matrix_1.7-4
INFO [2025-11-18 22:51:45] [10] zip_2.3.3 brio_1.1.5 formatR_1.14
INFO [2025-11-18 22:51:45] [13] purrr_1.2.0 viridisLite_0.4.2 scales_1.4.0
INFO [2025-11-18 22:51:45] [16] abind_1.4-8 cli_3.6.5 rlang_1.1.6
INFO [2025-11-18 22:51:45] [19] XVector_0.51.0 futile.logger_1.4.3 withr_3.0.2
INFO [2025-11-18 22:51:45] [22] DelayedArray_0.37.0 S4Arrays_1.11.0 tools_4.6.0
INFO [2025-11-18 22:51:45] [25] dplyr_1.1.4 lambda.r_1.2.4 vctrs_0.6.5
INFO [2025-11-18 22:51:45] [28] R6_2.6.1 lifecycle_1.0.4 pkgconfig_2.0.3
INFO [2025-11-18 22:51:45] [31] waldo_0.6.2 desc_1.4.3 pillar_1.11.1
INFO [2025-11-18 22:51:45] [34] openxlsx_4.2.8.1 gtable_0.3.6 glue_1.8.0
INFO [2025-11-18 22:51:45] [37] Rcpp_1.1.0 tibble_3.3.0 tidyselect_1.2.1
INFO [2025-11-18 22:51:45] [40] dichromat_2.0-0.1 farver_2.1.2 compiler_4.6.0
INFO [2025-11-18 22:51:45] [43] S7_0.2.1
INFO [2025-11-18 22:51:45] New line
INFO [2025-11-18 22:51:45] Starting logging
INFO [2025-11-18 22:51:45] New line
INFO [2025-11-18 22:51:45] Finished analysis. Tue Nov 18 22:51:45 2025
Session info:
INFO [2025-11-18 22:51:45] R Under development (unstable) (2025-10-21 r88958)
INFO [2025-11-18 22:51:45] Platform: x86_64-apple-darwin20
INFO [2025-11-18 22:51:45] Running under: macOS Ventura 13.7.8
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] Matrix products: default
INFO [2025-11-18 22:51:45] BLAS: /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libRblas.0.dylib
INFO [2025-11-18 22:51:45] LAPACK: /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] locale:
INFO [2025-11-18 22:51:45] [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] time zone: America/New_York
INFO [2025-11-18 22:51:45] tzcode source: internal
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] attached base packages:
INFO [2025-11-18 22:51:45] [1] stats4 stats graphics grDevices utils datasets methods
INFO [2025-11-18 22:51:45] [8] base
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] other attached packages:
INFO [2025-11-18 22:51:45] [1] notame_1.1.0 SummarizedExperiment_1.41.0
INFO [2025-11-18 22:51:45] [3] Biobase_2.71.0 GenomicRanges_1.63.0
INFO [2025-11-18 22:51:45] [5] Seqinfo_1.1.0 IRanges_2.45.0
INFO [2025-11-18 22:51:45] [7] S4Vectors_0.49.0 BiocGenerics_0.57.0
INFO [2025-11-18 22:51:45] [9] generics_0.1.4 MatrixGenerics_1.23.0
INFO [2025-11-18 22:51:45] [11] matrixStats_1.5.0 ggplot2_4.0.1
INFO [2025-11-18 22:51:45] [13] testthat_3.3.0
INFO [2025-11-18 22:51:45]
INFO [2025-11-18 22:51:45] loaded via a namespace (and not attached):
INFO [2025-11-18 22:51:45] [1] tidyr_1.3.1 futile.options_1.0.1 SparseArray_1.11.2
INFO [2025-11-18 22:51:45] [4] stringi_1.8.7 lattice_0.22-7 magrittr_2.0.4
INFO [2025-11-18 22:51:45] [7] grid_4.6.0 RColorBrewer_1.1-3 Matrix_1.7-4
INFO [2025-11-18 22:51:45] [10] zip_2.3.3 brio_1.1.5 formatR_1.14
INFO [2025-11-18 22:51:45] [13] purrr_1.2.0 viridisLite_0.4.2 scales_1.4.0
INFO [2025-11-18 22:51:45] [16] abind_1.4-8 cli_3.6.5 rlang_1.1.6
INFO [2025-11-18 22:51:45] [19] XVector_0.51.0 futile.logger_1.4.3 withr_3.0.2
INFO [2025-11-18 22:51:45] [22] DelayedArray_0.37.0 S4Arrays_1.11.0 tools_4.6.0
INFO [2025-11-18 22:51:45] [25] dplyr_1.1.4 lambda.r_1.2.4 vctrs_0.6.5
INFO [2025-11-18 22:51:45] [28] R6_2.6.1 lifecycle_1.0.4 pkgconfig_2.0.3
INFO [2025-11-18 22:51:45] [31] waldo_0.6.2 desc_1.4.3 pillar_1.11.1
INFO [2025-11-18 22:51:45] [34] openxlsx_4.2.8.1 gtable_0.3.6 glue_1.8.0
INFO [2025-11-18 22:51:45] [37] Rcpp_1.1.0 tibble_3.3.0 tidyselect_1.2.1
INFO [2025-11-18 22:51:45] [40] dichromat_2.0-0.1 farver_2.1.2 compiler_4.6.0
INFO [2025-11-18 22:51:45] [43] S7_0.2.1
INFO [2025-11-18 22:51:45] New line
INFO [2025-11-18 22:51:45]
Starting random forest imputation at 2025-11-18 22:51:45.798626
INFO [2025-11-18 22:51:49] Out-of-bag error in random forest imputation: 0.467
INFO [2025-11-18 22:51:49] Random forest imputation finished at 2025-11-18 22:51:49.412582
INFO [2025-11-18 22:51:49]
Starting random forest imputation at 2025-11-18 22:51:49.67978
INFO [2025-11-18 22:51:52] Out-of-bag error in random forest imputation: 0.472
INFO [2025-11-18 22:51:52] Random forest imputation finished at 2025-11-18 22:51:52.429098
INFO [2025-11-18 22:51:52]
Starting random forest imputation at 2025-11-18 22:51:52.447204
INFO [2025-11-18 22:51:54] Out-of-bag error in random forest imputation: 0.469
INFO [2025-11-18 22:51:54] Random forest imputation finished at 2025-11-18 22:51:54.768258
INFO [2025-11-18 22:51:54]
Starting random forest imputation at 2025-11-18 22:51:54.819686
INFO [2025-11-18 22:51:57] Out-of-bag error in random forest imputation: 0.468
INFO [2025-11-18 22:51:57] Random forest imputation finished at 2025-11-18 22:51:57.179159
INFO [2025-11-18 22:51:57] Starting PQN normalization
INFO [2025-11-18 22:51:57] Using median of qc samples as reference spectrum
INFO [2025-11-18 22:51:57] Starting PQN normalization
INFO [2025-11-18 22:51:57] Using median of all samples as reference spectrum
INFO [2025-11-18 22:51:57] Starting PQN normalization
INFO [2025-11-18 22:51:57] Using mean of qc samples as reference spectrum
INFO [2025-11-18 22:51:57] Starting PQN normalization
INFO [2025-11-18 22:51:57] Using mean of all samples as reference spectrum
INFO [2025-11-18 22:51:57]
92% of features flagged for low quality
INFO [2025-11-18 22:51:57] Starting PQN normalization
INFO [2025-11-18 22:51:57] Using median of qc samples as reference spectrum
INFO [2025-11-18 22:51:58] Starting drift correction
INFO [2025-11-18 22:51:58] Zero values in feature abundances detected. Zeroes will be replaced with 1.1.
INFO [2025-11-18 22:52:01] Recomputing quality metrics for drift corrected data
INFO [2025-11-18 22:52:01] Drift correction performed
INFO [2025-11-18 22:52:01] Inspecting drift correction results
INFO [2025-11-18 22:52:01] Original quality metrics missing, recomputing
INFO [2025-11-18 22:52:01] 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
31.279 4.772 30.294
notame.Rcheck/notame-Ex.timings
| name | user | system | elapsed | |
| assess_quality | 0.209 | 0.023 | 0.232 | |
| citations | 0.316 | 0.029 | 0.348 | |
| cluster_features | 0.262 | 0.041 | 0.306 | |
| combined_data | 0.057 | 0.031 | 0.088 | |
| compress_clusters | 0.153 | 0.023 | 0.175 | |
| correct_drift | 3.403 | 0.398 | 3.558 | |
| drop_flagged | 0.132 | 0.018 | 0.152 | |
| drop_qcs | 0.044 | 0.009 | 0.052 | |
| finish_log | 0.033 | 0.014 | 0.048 | |
| fix_MSMS | 0.118 | 0.020 | 0.139 | |
| fix_object | 0.143 | 0.018 | 0.163 | |
| flag | 0.033 | 0.012 | 0.045 | |
| flag_contaminants | 0.222 | 0.024 | 0.247 | |
| flag_detection | 0.255 | 0.014 | 0.269 | |
| flag_quality | 0.236 | 0.010 | 0.247 | |
| flag_report | 0.358 | 0.007 | 0.367 | |
| import_from_excel | 0.289 | 0.032 | 0.328 | |
| impute_rf | 3.051 | 0.825 | 2.576 | |
| impute_simple | 0.100 | 0.005 | 0.107 | |
| init_log | 0.003 | 0.001 | 0.005 | |
| inverse_normalize | 0.045 | 0.004 | 0.050 | |
| join_colData | 0.037 | 0.005 | 0.043 | |
| join_rowData | 0.027 | 0.005 | 0.032 | |
| log_text | 0.005 | 0.001 | 0.005 | |
| mark_nas | 0.045 | 0.003 | 0.048 | |
| merge_notame_sets | 0.515 | 0.010 | 0.526 | |
| pca_bhattacharyya_dist | 7.570 | 0.824 | 8.453 | |
| perform_repeatability | 0.222 | 0.007 | 0.230 | |
| pqn_normalization | 0.079 | 0.005 | 0.086 | |
| quality | 0.093 | 0.012 | 0.105 | |
| ruvs_qc | 0.190 | 0.026 | 0.216 | |
| write_to_excel | 0.244 | 0.046 | 0.296 | |