Christophe Vanderaa
| Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/scp |
| git_branch: devel |
| git_last_commit: 3ef39c3 |
| git_last_commit_date: 2025-10-14 16:15:34 -0400 (Tue, 14 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-23 12:05 -0400 (Thu, 23 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4894 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4684 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4629 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1939/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scp 1.19.5 (landing page) Christophe Vanderaa
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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: 1.19.5 |
| 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_1.19.5.tar.gz |
| StartedAt: 2025-10-23 00:00:35 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 00:10:40 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 604.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scp.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.19.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scp.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scp/DESCRIPTION’ ... OK
* this is package ‘scp’ version ‘1.19.5’
* 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 ... WARNING
Missing link(s) in Rd file 'scplainer.Rd':
‘scpModel-Workflow’
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
scplainer.Rd: SingleCellExperiment, scpModel-Workflow
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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ScpModel-Workflow 11.974 0.062 12.075
aggregateFeaturesOverAssays-deprecated 7.929 0.103 8.068
ScpModel-DifferentialAnalysis 5.088 0.042 5.152
* 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 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-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-x86_64/Resources/library’ * installing *source* package ‘scp’ ... ** this is package ‘scp’ version ‘1.19.5’ ** 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
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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("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: 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
Attaching package: 'QFeatures'
The following object is masked from 'package:base':
sweep
>
> test_check("scp")
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[ FAIL 0 | WARN 3 | SKIP 13 | PASS 850 ]
══ Skipped tests (13) ══════════════════════════════════════════════════════════
• On CRAN (13): 'test-ScpModel-ComponentAnalysis.R:788:5',
'test-ScpModel-ComponentAnalysis.R:848:5',
'test-ScpModel-ComponentAnalysis.R:931:5',
'test-ScpModel-ComponentAnalysis.R:959:5',
'test-ScpModel-ComponentAnalysis.R:1076:5',
'test-ScpModel-DifferentialAnalysis.R:787:5',
'test-ScpModel-DifferentialAnalysis.R:899:5',
'test-ScpModel-VarianceAnalysis.R:246:5',
'test-ScpModel-VarianceAnalysis.R:380:5',
'test-ScpModel-VarianceAnalysis.R:401:5',
'test-ScpModel-VarianceAnalysis.R:420:5', 'test-ScpModel-Workflow.R:765:5',
'test-ScpModel-Workflow.R:806:5'
[ FAIL 0 | WARN 3 | SKIP 13 | PASS 850 ]
>
> proc.time()
user system elapsed
295.743 8.198 313.407
scp.Rcheck/scp-Ex.timings
| name | user | system | elapsed | |
| ScpModel-ComponentAnalysis | 3.506 | 0.079 | 3.609 | |
| ScpModel-DataCorrection | 0.890 | 0.014 | 0.906 | |
| ScpModel-DifferentialAnalysis | 5.088 | 0.042 | 5.152 | |
| ScpModel-VarianceAnalysis | 4.907 | 0.029 | 4.957 | |
| ScpModel-Workflow | 11.974 | 0.062 | 12.075 | |
| ScpModel-class | 1.077 | 0.010 | 1.095 | |
| ScpModelFit-class | 0.003 | 0.000 | 0.003 | |
| addReducedDims | 2.423 | 0.091 | 2.536 | |
| aggregateFeaturesOverAssays-deprecated | 7.929 | 0.103 | 8.068 | |
| computeSCR | 0.088 | 0.004 | 0.093 | |
| cumulativeSensitivityCurve | 1.021 | 0.039 | 1.077 | |
| divideByReference | 0.138 | 0.003 | 0.142 | |
| jaccardIndex | 0.159 | 0.015 | 0.175 | |
| medianCVperCell | 0.517 | 0.016 | 0.540 | |
| normalizeSCP | 0.174 | 0.004 | 0.178 | |
| pep2qvalue | 0.273 | 0.004 | 0.277 | |
| readSCP | 0.569 | 0.012 | 0.583 | |
| reportMissingValues | 0.160 | 0.006 | 0.166 | |
| scp1 | 0.040 | 0.003 | 0.043 | |
| scpAnnotateResults | 0.605 | 0.009 | 0.616 | |