| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-16 11:58 -0500 (Mon, 16 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4889 |
| 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 1945/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scp 1.20.0 (landing page) Christophe Vanderaa
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for scp in R Universe. | ||||||||||||||
|
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: 1.20.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scp.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scp_1.20.0.tar.gz |
| StartedAt: 2026-02-13 05:05:11 -0500 (Fri, 13 Feb 2026) |
| EndedAt: 2026-02-13 05:23:29 -0500 (Fri, 13 Feb 2026) |
| EllapsedTime: 1097.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: scp.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scp.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scp_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scp.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘scp/DESCRIPTION’ ... OK
* this is package ‘scp’ version ‘1.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/PACKAGES'
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 loading without being on the library search path ... 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 8.664 0.030 8.695
aggregateFeaturesOverAssays-deprecated 5.163 0.075 5.238
* 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:
1. ├─utils::read.delim(MsDataHub::Report.Derks2022.plexDIA.tsv()) at test-readSCP.R:36:5
2. │ └─utils::read.table(...)
3. └─MsDataHub::Report.Derks2022.plexDIA.tsv()
4. └─ExperimentHub:::.get_ExperimentHub()
5. └─ExperimentHub::ExperimentHub()
6. └─AnnotationHub::.Hub(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─value[[3L]](cond)
[ FAIL 2 | WARN 3 | SKIP 13 | PASS 851 ]
Error:
! Test failures.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘QFeatures_nutshell.Rmd’ using rmarkdown
--- finished re-building ‘QFeatures_nutshell.Rmd’
--- re-building ‘advanced.Rmd’ using rmarkdown
--- finished re-building ‘advanced.Rmd’
--- re-building ‘read_scp.Rmd’ using rmarkdown
--- finished re-building ‘read_scp.Rmd’
--- re-building ‘reporting_missing_values.Rmd’ using rmarkdown
Quitting from reporting_missing_values.Rmd:56-60 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
Consider rerunning with 'localHub=TRUE'
---
Backtrace:
▆
1. └─scpdata::leduc2022()
2. └─ExperimentHub (local) leduc2022_pSCoPE()
3. └─ExperimentHub:::.get_ExperimentHub()
4. └─ExperimentHub::ExperimentHub()
5. └─AnnotationHub::.Hub(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'reporting_missing_values.Rmd' failed with diagnostics:
failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘reporting_missing_values.Rmd’
--- re-building ‘scp.Rmd’ using rmarkdown
--- finished re-building ‘scp.Rmd’
--- re-building ‘scp_data_modelling.Rmd’ using rmarkdown
Warning: ggrepel: 13 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘scp_data_modelling.Rmd’
SUMMARY: processing the following file failed:
‘reporting_missing_values.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/scp.Rcheck/00check.log’
for details.
scp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scp ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘scp’ ... ** this is package ‘scp’ version ‘1.20.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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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Saving _problems/test-readSCP-28.R
Saving _problems/test-readSCP-36.R
[ FAIL 2 | WARN 3 | SKIP 13 | PASS 851 ]
══ Skipped tests (13) ══════════════════════════════════════════════════════════
• On CRAN (13): 'test-ScpModel-ComponentAnalysis.R:769:1',
'test-ScpModel-ComponentAnalysis.R:832:1',
'test-ScpModel-ComponentAnalysis.R:905:1',
'test-ScpModel-ComponentAnalysis.R:937:1',
'test-ScpModel-ComponentAnalysis.R:1060:1',
'test-ScpModel-DifferentialAnalysis.R:771:1',
'test-ScpModel-DifferentialAnalysis.R:891:1',
'test-ScpModel-VarianceAnalysis.R:232:1',
'test-ScpModel-VarianceAnalysis.R:368:1',
'test-ScpModel-VarianceAnalysis.R:391:1',
'test-ScpModel-VarianceAnalysis.R:407:1', 'test-ScpModel-Workflow.R:750:1',
'test-ScpModel-Workflow.R:804:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-readSCP.R:28:5'): readSCPfromDIANN ─────────────────────────────
Error in `value[[3L]](cond)`: failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
Consider rerunning with 'localHub=TRUE'
Backtrace:
▆
1. ├─utils::read.delim(MsDataHub::Report.Derks2022.plexDIA.tsv()) at test-readSCP.R:28:5
2. │ └─utils::read.table(...)
3. └─MsDataHub::Report.Derks2022.plexDIA.tsv()
4. └─ExperimentHub:::.get_ExperimentHub()
5. └─ExperimentHub::ExperimentHub()
6. └─AnnotationHub::.Hub(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─value[[3L]](cond)
── Error ('test-readSCP.R:36:5'): readSCPfromDIANN with sce ────────────────────
Error in `value[[3L]](cond)`: failed to connect
reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
Consider rerunning with 'localHub=TRUE'
Backtrace:
▆
1. ├─utils::read.delim(MsDataHub::Report.Derks2022.plexDIA.tsv()) at test-readSCP.R:36:5
2. │ └─utils::read.table(...)
3. └─MsDataHub::Report.Derks2022.plexDIA.tsv()
4. └─ExperimentHub:::.get_ExperimentHub()
5. └─ExperimentHub::ExperimentHub()
6. └─AnnotationHub::.Hub(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─value[[3L]](cond)
[ FAIL 2 | WARN 3 | SKIP 13 | PASS 851 ]
Error:
! Test failures.
Execution halted
scp.Rcheck/scp-Ex.timings
| name | user | system | elapsed | |
| ScpModel-ComponentAnalysis | 3.025 | 0.043 | 3.068 | |
| ScpModel-DataCorrection | 0.737 | 0.000 | 0.737 | |
| ScpModel-DifferentialAnalysis | 3.998 | 0.136 | 4.134 | |
| ScpModel-VarianceAnalysis | 3.667 | 0.059 | 3.727 | |
| ScpModel-Workflow | 8.664 | 0.030 | 8.695 | |
| ScpModel-class | 0.795 | 0.014 | 0.809 | |
| ScpModelFit-class | 0.002 | 0.000 | 0.002 | |
| addReducedDims | 1.828 | 0.049 | 1.877 | |
| aggregateFeaturesOverAssays-deprecated | 5.163 | 0.075 | 5.238 | |
| computeSCR | 0.076 | 0.002 | 0.078 | |
| cumulativeSensitivityCurve | 1.523 | 0.094 | 1.617 | |
| divideByReference | 0.113 | 0.002 | 0.115 | |
| jaccardIndex | 0.134 | 0.014 | 0.148 | |
| medianCVperCell | 0.370 | 0.052 | 0.422 | |
| normalizeSCP | 0.127 | 0.000 | 0.128 | |
| pep2qvalue | 0.218 | 0.003 | 0.221 | |
| readSCP | 0.447 | 0.025 | 0.472 | |
| reportMissingValues | 0.123 | 0.016 | 0.139 | |
| scp1 | 0.035 | 0.001 | 0.037 | |
| scpAnnotateResults | 0.478 | 0.038 | 0.516 | |