• using R Under development (unstable) (2025-03-10 r87922)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-17) 14.2.0     GNU Fortran (Debian 14.2.0-17) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘RAMClustR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘RAMClustR’ version ‘1.3.1’
• package encoding: UTF-8
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• checking whether package ‘RAMClustR’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
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• checking R files for syntax errors ... OK
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• checking examples ... [2s/2s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [28s/36s] ERROR   Running ‘testthat.R’ [28s/35s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(RAMClustR)   >   > test_check("RAMClustR")   plotting findmain annotation results   finished   87.5% of features move forward   ma MSdata   df phenoData   Features which failed to demonstrate signal intensity of at least 3 fold greater in QC samples than in blanks were removed from the feature dataset. 6 of 48 features were removed.MSdata : 33 passed the CV filter   Features were filtered based on their qc sample CV values. Only features with CV vaules less than or equal to 0.5 in MSdata set were retained. 9 of 42 features were removed.Features were normalized by linearly regressing run order versus qc feature intensities to account for instrument signal intensity drift. Only features with a regression pvalue less than 0.05 and an r-squared greater than 0.1 were corrected. Of 42 features, 0 was corrected for run order effects.replaced 12 of 192 total feature values ( 6 % )   Calculating ramclustR similarity using 3 nblocks.   1    RAMClust feature similarity matrix calculated and stored.   fastcluster based clustering complete   dynamicTreeCut based pruning complete   RAMClust has condensed 33 features into 4 spectra   collapsing feature into spectral signal intensities   Calculating ramclustR similarity using 3 nblocks.   1    RAMClust feature similarity matrix calculated and stored.   fastcluster based clustering complete   dynamicTreeCut based pruning complete   RAMClust has condensed 33 features into 6 spectra   collapsing feature into spectral signal intensities   organizing dataset   organizing dataset   [ FAIL 5 | WARN 10 | SKIP 0 | PASS 17 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-rc.get.xcms.data.R:7:3'): RAMClustR rc.get.xcms.data ───────────   Error in `xcmsObj@phenoData[[1]]`: this S4 class is not subsettable   Backtrace:       ▆    1. └─RAMClustR::rc.get.xcms.data(xcmsObj = xdata) at test-rc.get.xcms.data.R:7:3   ── Error ('test-stepwise-workflow.R:11:3'): RAMClustR workflow with xcms works ──   Error in `xcmsObj@phenoData[[1]]`: this S4 class is not subsettable   Backtrace:       ▆    1. └─RAMClustR::rc.get.xcms.data(xcmsObj = xdata) at test-stepwise-workflow.R:11:3   ── Error ('test-workflow-comparison.R:8:3'): RAMClustR workflow comparison test ──   Error in `xcmsObj@phenoData[[1]]`: this S4 class is not subsettable   Backtrace:       ▆    1. └─RAMClustR::ramclustR(xcmsObj = xdata, maxt = 20, sr = 0.5) at test-workflow-comparison.R:8:3    2. └─RAMClustR::rc.get.xcms.data(...)   ── Error ('test.R:11:3'): RAMClustR with xcms works ────────────────────────────   Error in `xcmsObj@phenoData[[1]]`: this S4 class is not subsettable   Backtrace:       ▆    1. └─RAMClustR::ramclustR(xcmsObj = xdata, maxt = 20, sr = 0.5, mzdec = 4) at test.R:11:3    2. └─RAMClustR::rc.get.xcms.data(...)   ── Error ('test.R:24:3'): RAMClustR with csv works ─────────────────────────────   Error in `gzfile(file, "rb")`: cannot open the connection   Backtrace:       ▆    1. └─base::readRDS(file.path("testdata", "test_csv.rds")) at test.R:24:3    2. └─base::gzfile(file, "rb")      [ FAIL 5 | WARN 10 | SKIP 0 | PASS 17 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
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• checking re-building of vignette outputs ... [2s/2s] OK
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [1s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR