Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1958/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
signifinder 1.8.0 (landing page) Stefania Pirrotta
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the signifinder package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/signifinder.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: signifinder |
Version: 1.8.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signifinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signifinder_1.8.0.tar.gz |
StartedAt: 2024-12-21 09:29:04 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 09:41:48 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 763.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: signifinder.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signifinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signifinder_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/signifinder.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘signifinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘signifinder’ version ‘1.8.0’ * 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 ‘signifinder’ 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 ... OK * 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 ... OK * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘signifinder-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ADOSign > ### Title: Adenosine Signaling Signature > ### Aliases: ADOSign > > ### ** Examples > > data(ovse) > ADOSign(dataset = ovse) ADOSign is using 100% of signature genes ! 3 genes with constant values throughout the samples ! Genes with constant values are discarded Error in `.mapGeneSetsToFeatures()`: ✖ No identifiers in the gene sets could be matched to the identifiers in the expression data. Backtrace: ▆ 1. └─signifinder::ADOSign(dataset = ovse) 2. ├─base::as.vector(gsva(gsvaPar, verbose = FALSE)) 3. ├─GSVA::gsva(gsvaPar, verbose = FALSE) 4. └─GSVA::gsva(gsvaPar, verbose = FALSE) 5. └─GSVA (local) .local(param, ...) 6. ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM) 7. └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM) 8. └─GSVA (local) .local(param, ...) 9. └─GSVA:::.filterAndMapGeneSets(...) 10. └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix)) 11. └─cli::cli_abort(c(x = msg)) 12. └─rlang::abort(...) Execution halted * 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: 2. ├─base::as.vector(gsva(gsvaPar, verbose = FALSE)) 3. ├─GSVA::gsva(gsvaPar, verbose = FALSE) 4. └─GSVA::gsva(gsvaPar, verbose = FALSE) 5. └─GSVA (local) .local(param, ...) 6. ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM) 7. └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM) 8. └─GSVA (local) .local(param, ...) 9. └─GSVA:::.filterAndMapGeneSets(...) 10. └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix)) 11. └─cli::cli_abort(c(x = msg)) 12. └─rlang::abort(...) [ FAIL 2 | WARN 10 | SKIP 0 | PASS 260 ] 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: 2 ERRORs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/signifinder.Rcheck/00check.log’ for details.
signifinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL signifinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘signifinder’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (signifinder)
signifinder.Rcheck/tests/testthat.Rout.fail
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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(signifinder) > > test_check("signifinder") 'select()' returned 1:1 mapping between keys and columns Loading required package: edgeR Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA pyroptosisSignYe is using 100% of signature genes 'select()' returned 1:1 mapping between keys and columns ferroptosisSignLiu is using 100% of signature genes lipidMetabolismSign is using 100% of signature genes StemCellCD49fSign is using 100% of signature genes glycolysisSignZhang is using 100% of signature genes autophagySignWang is using 100% of signature genes 'select()' returned 1:1 mapping between keys and columns autophagySignChenM is using 27% of OS signature genes autophagySignChenM is using 100% of DFS signature genes TinflamSign is using 100% of signature genes EMTSignMiow is using 0% of epithelial signature genes EMTSignMiow is using 100% of mesenchymal signature genes EMTSignMiow is using 0% of epithelial signature genes EMTSignMak is using 100% of epithelial signature genes EMTSignMak is using 100% of mesenchymal signature genes EMTSignMak is using 100% of mesenchymal signature genes EMTSignCheng is using 100% of signature genes EMTSignThompson is using 100% of epithelial signature genes EMTSignThompson is using 100% of mesenchymal signature genes 'select()' returned 1:1 mapping between keys and columns EMTSignThompson is using 100% of mesenchymal signature genes 'select()' returned 1:1 mapping between keys and columns ASCSign is using 100% of signature genes ChemokineSign is using 100% of signature genes 'select()' returned 1:1 mapping between keys and columns PassONSign is using 100% of signature genes CISSign is using 100% of up signature genes CISSign is using 100% of down signature genes CISSign is using 100% of down signature genes HRDSSign is using 100% of signature genes DNArepSign is using 100% of signature genes 'select()' returned 1:1 mapping between keys and columns IPRESSign is using 100% of signature genes ! Input expression data has NA values, which will be propagated through calculations. ECMSign is using 0% of up signature genes ECMSign is using 100% of down signature genes ECMSign is using 0% of up signature genes IPSOVSign is using 100% of signature genes ! Duplicated gene IDs removed from gene set Antimicrobials ! Some gene sets have size one. Consider setting minSize > 1 ! Duplicated gene IDs removed from gene set Antimicrobials ! Some gene sets have size one. Consider setting minSize > 1 'select()' returned 1:1 mapping between keys and columns glioCellStateSign is using 100% of MES2 signature genes glioCellStateSign is using 100% of MES1 signature genes glioCellStateSign is using 100% of AC signature genes glioCellStateSign is using 100% of OPC signature genes glioCellStateSign is using 100% of NPC1 signature genes glioCellStateSign is using 100% of NPC2 signature genes TinflamSignThompson is using 100% of signature genes 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns EMTSignThompson is using 100% of epithelial signature genes EMTSignThompson is using 100% of mesenchymal signature genes 'select()' returned 1:1 mapping between keys and columns TinflamSignThompson is using 100% of signature genes 'select()' returned 1:1 mapping between keys and columns EMTSignThompson is using 100% of mesenchymal signature genes 'select()' returned 1:1 mapping between keys and columns TinflamSignThompson is using 100% of signature genes 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns melStateSign is using 100% of MITF signature genes melStateSign is using 100% of AXL signature genes 'select()' returned 1:1 mapping between keys and columns APMSign is using 100% of signature genes 'select()' returned 1:1 mapping between keys and columns APMSign is using 100% of signature genes 'select()' returned 1:1 mapping between keys and columns MPSSign is using 100% of signature genes 'select()' returned 1:1 mapping between keys and columns IRGSign is using 100% of signature genes TGFBSign is using 100% of signature genes ADOSign is using 100% of signature genes MITFlowPTENnegSign is using 100% of signature genes LRRC15CAFSign is using 100% of signature genes breastStateSign is using 100% of Basal signature genes breastStateSign is using 100% of Her2E signature genes breastStateSign is using 100% of LumA signature genes breastStateSign is using 100% of LumB signature genes breastStateSign is using 100% of Her2E signature genes breastStateSign is using 100% of LumA signature genes breastStateSign is using 100% of LumB signature genes ICBResponseSign is using 100% of responder signature genes ICBResponseSign is using 0% of nonresponder signature genes ICBResponseSign is using 0% of nonresponder signature genes COXISSign is using 100% of signature genes TLSSign is using 100% of signature genes expandedImmuneSign is using 100% of signature genes IFNSign is using 100% of signature genes ImmuneCytSignRooney is using 100% of signature genes mitoticIndexSign is using 100% of signature genes matrisomeSign is using 100% of signature genes immunoScoreSignRoh is using 100% of signature genes CINSign is using 100% of signature genes CINSign is using 36% of signature genes CINSign is using 36% of signature genes hypoxiaSign is using 100% of signature genes cellCycleSignLundberg is using 100% of signature genes cellCycleSignDavoli is using 100% of signature genes VEGFSign is using 100% of signature genes ImmuneCytSignDavoli is using 100% of signature genes [ FAIL 2 | WARN 10 | SKIP 0 | PASS 260 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-SignatureFunctions.R:193:3'): APMSign based on Wang's work ───── Error in `.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))`: x No identifiers in the gene sets could be matched to the identifiers in the expression data. Backtrace: ▆ 1. └─signifinder::APMSign(rmatrix) at test-SignatureFunctions.R:193:3 2. ├─GSVA::gsva(gsvaPar, verbose = FALSE) 3. └─GSVA::gsva(gsvaPar, verbose = FALSE) 4. └─GSVA (local) .local(param, ...) 5. ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM) 6. └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM) 7. └─GSVA (local) .local(param, ...) 8. └─GSVA:::.filterAndMapGeneSets(...) 9. └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix)) 10. └─cli::cli_abort(c(x = msg)) 11. └─rlang::abort(...) ── Error ('test-SignatureFunctions.R:233:3'): ADOSign work ───────────────────── Error in `.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))`: x No identifiers in the gene sets could be matched to the identifiers in the expression data. Backtrace: ▆ 1. └─signifinder::ADOSign(rmatrix) at test-SignatureFunctions.R:233:3 2. ├─base::as.vector(gsva(gsvaPar, verbose = FALSE)) 3. ├─GSVA::gsva(gsvaPar, verbose = FALSE) 4. └─GSVA::gsva(gsvaPar, verbose = FALSE) 5. └─GSVA (local) .local(param, ...) 6. ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM) 7. └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM) 8. └─GSVA (local) .local(param, ...) 9. └─GSVA:::.filterAndMapGeneSets(...) 10. └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix)) 11. └─cli::cli_abort(c(x = msg)) 12. └─rlang::abort(...) [ FAIL 2 | WARN 10 | SKIP 0 | PASS 260 ] Error: Test failures Execution halted
signifinder.Rcheck/signifinder-Ex.timings
name | user | system | elapsed |