Last updated on 2025-03-09 05:52:40 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 | 13.17 | 151.85 | 165.02 | 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 |
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