Christophe Vanderaa
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/scp |
| git_branch: RELEASE_3_21 |
| git_last_commit: d05ad64 |
| git_last_commit_date: 2025-04-15 12:11:18 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 1928/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scp 1.18.0 (landing page) Christophe Vanderaa
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the scp package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scp.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: scp |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scp_1.18.0.tar.gz |
| StartedAt: 2025-04-21 21:32:45 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 21:35:35 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 170.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: scp.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scp_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scp.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scp/DESCRIPTION’ ... OK
* this is package ‘scp’ version ‘1.18.0’
* 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 ‘scp’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘MultiAssayExperiment:::.sampleMapFromData’ ‘QFeatures:::.get_Hits’
‘QFeatures:::.normIndex’
See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'ScpModel-ComponentAnalysis.Rd':
‘[QFeatures:QFeatures-aggregate]{QFeatures::aggregateFeatures()}’
Non-topic package-anchored link(s) in Rd file 'addReducedDims.Rd':
‘[scater:plot_reddim]{scater::plotTSNE()}’
Non-topic package-anchored link(s) in Rd file 'aggregateFeaturesOverAssays-deprecated.Rd':
‘[QFeatures:QFeatures-aggregate]{QFeatures::aggregateFeatures}’
Non-topic package-anchored link(s) in Rd file 'medianCVperCell.Rd':
‘[MsCoreUtils:normalize]{MsCoreUtils::normalizeMethods}’
Non-topic package-anchored link(s) in Rd file 'normalizeSCP.Rd':
‘[MsCoreUtils:normalize]{MsCoreUtils::normalizeMethods()}’
‘[MsCoreUtils:normalize]{MsCoreUtils::normalize_matrix()}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
addReducedDims.Rd: SingleCellExperiment
cumulativeSensitivityCurve.Rd: QFeatures
jaccardIndex.Rd: QFeatures
mqScpData.Rd: QFeatures
readSCP.Rd: readSummarizedExperiment, readQFeatures,
readQFeaturesFromDIANN
reportMissingValues.Rd: QFeatures
scp1.Rd: QFeatures, SingleCellExperiment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
'test-ScpModel-VarianceAnalysis.R:400:5',
'test-ScpModel-VarianceAnalysis.R:419:5', 'test-ScpModel-Workflow.R:765:5',
'test-ScpModel-Workflow.R:806:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-compute_metrics.R:158:5'): computeSCR ────────────────────────
rowData(test[[2]])$SCR not identical to unname(...).
Objects equal but not identical
── Failure ('test-compute_metrics.R:166:5'): computeSCR ────────────────────────
rowData(test[[2]])$medianSCR not identical to unname(...).
Objects equal but not identical
[ FAIL 2 | WARN 3 | SKIP 13 | PASS 836 ]
Error: Test failures
Execution halted
* 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 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/scp.Rcheck/00check.log’
for details.
scp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scp ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘scp’ ... ** this is package ‘scp’ version ‘1.18.0’ ** 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 (scp)
scp.Rcheck/tests/testthat.Rout.fail
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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("vdiffr")
> library("scp")
Loading required package: QFeatures
Loading required package: MultiAssayExperiment
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: GenomeInfoDb
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
Attaching package: 'QFeatures'
The following object is masked from 'package:base':
sweep
>
> test_check("scp")
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[ FAIL 2 | WARN 3 | SKIP 13 | PASS 836 ]
══ Skipped tests (13) ══════════════════════════════════════════════════════════
• On CRAN (13): 'test-ScpModel-ComponentAnalysis.R:787:5',
'test-ScpModel-ComponentAnalysis.R:847:5',
'test-ScpModel-ComponentAnalysis.R:930:5',
'test-ScpModel-ComponentAnalysis.R:958:5',
'test-ScpModel-ComponentAnalysis.R:1075:5',
'test-ScpModel-DifferentialAnalysis.R:786:5',
'test-ScpModel-DifferentialAnalysis.R:898:5',
'test-ScpModel-VarianceAnalysis.R:245:5',
'test-ScpModel-VarianceAnalysis.R:379:5',
'test-ScpModel-VarianceAnalysis.R:400:5',
'test-ScpModel-VarianceAnalysis.R:419:5', 'test-ScpModel-Workflow.R:765:5',
'test-ScpModel-Workflow.R:806:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-compute_metrics.R:158:5'): computeSCR ────────────────────────
rowData(test[[2]])$SCR not identical to unname(...).
Objects equal but not identical
── Failure ('test-compute_metrics.R:166:5'): computeSCR ────────────────────────
rowData(test[[2]])$medianSCR not identical to unname(...).
Objects equal but not identical
[ FAIL 2 | WARN 3 | SKIP 13 | PASS 836 ]
Error: Test failures
Execution halted
scp.Rcheck/scp-Ex.timings
| name | user | system | elapsed | |
| ScpModel-ComponentAnalysis | 1.097 | 0.020 | 1.156 | |
| ScpModel-DataCorrection | 0.253 | 0.002 | 0.259 | |
| ScpModel-DifferentialAnalysis | 0.880 | 0.007 | 0.889 | |
| ScpModel-VarianceAnalysis | 1.107 | 0.015 | 1.141 | |
| ScpModel-Workflow | 3.318 | 0.015 | 3.370 | |
| ScpModel-class | 0.280 | 0.002 | 0.282 | |
| ScpModelFit-class | 0.000 | 0.000 | 0.001 | |
| addReducedDims | 0.635 | 0.037 | 0.676 | |
| aggregateFeaturesOverAssays-deprecated | 1.801 | 0.004 | 1.813 | |
| computeSCR | 0.047 | 0.002 | 0.048 | |
| cumulativeSensitivityCurve | 0.344 | 0.016 | 0.359 | |
| divideByReference | 0.067 | 0.002 | 0.069 | |
| jaccardIndex | 0.081 | 0.008 | 0.102 | |
| medianCVperCell | 0.305 | 0.003 | 0.308 | |
| normalizeSCP | 0.090 | 0.002 | 0.092 | |
| pep2qvalue | 0.106 | 0.001 | 0.108 | |
| readSCP | 0.213 | 0.006 | 0.219 | |
| reportMissingValues | 0.064 | 0.002 | 0.065 | |
| scp1 | 0.016 | 0.001 | 0.018 | |
| scpAnnotateResults | 0.169 | 0.002 | 0.170 | |