CRAN Package Check Results for Package RAMClustR

Last updated on 2025-03-09 12:51:54 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.3.1	11.42	161.85	173.27	OK
r-devel-linux-x86_64-debian-gcc	1.3.1	8.13	95.86	103.99	ERROR
r-devel-linux-x86_64-fedora-clang	1.3.1			257.81	ERROR
r-devel-linux-x86_64-fedora-gcc	1.3.1			259.19	ERROR
r-devel-macos-arm64	1.3.1			53.00	OK
r-devel-macos-x86_64	1.3.1			112.00	OK
r-devel-windows-x86_64	1.3.1	17.00	172.00	189.00	OK
r-patched-linux-x86_64	1.3.1	14.43	151.38	165.81	OK
r-release-linux-x86_64	1.3.1	12.57	152.41	164.98	OK
r-release-macos-arm64	1.3.1			86.00	OK
r-release-macos-x86_64	1.3.1			137.00	OK
r-release-windows-x86_64	1.3.1	16.00	158.00	174.00	OK
r-oldrel-macos-arm64	1.3.1				NOTE
r-oldrel-macos-x86_64	1.3.1			103.00	NOTE
r-oldrel-windows-x86_64	1.3.1	20.00	203.00	223.00	OK

Check Details

Version: 1.3.1
Check: tests
Result: ERROR Running ‘testthat.R’ [28s/34s] 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 Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.3.1
Check: tests
Result: ERROR Running ‘testthat.R’ [55s/139s] 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 Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.3.1
Check: tests
Result: ERROR Running ‘testthat.R’ [51s/139s] 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 Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.3.1
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'xcms', 'MSnbase' Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64