Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 270/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
canceR 1.40.0 (landing page) Karim Mezhoud
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the canceR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/canceR.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: canceR |
Version: 1.40.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings canceR_1.40.0.tar.gz |
StartedAt: 2024-11-19 23:51:04 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 23:58:36 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 452.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: canceR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings canceR_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/canceR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘canceR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘canceR’ version ‘1.40.0’ * 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 ‘canceR’ 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 ... 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 ... NOTE S3 methods shown with full name in Rd file 'cbind.na.Rd': ‘cbind.na’ S3 methods shown with full name in Rd file 'rbind.na.Rd': ‘rbind.na’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... NOTE Argument items with no description in Rd file 'GSEA.EnrichmentScore.Rd': ‘gene.list’ ‘gene.set’ ‘weighted.score.type’ ‘correl.vector’ Argument items with no description in Rd file 'GSEA.EnrichmentScore2.Rd': ‘gene.list’ ‘gene.set’ ‘weighted.score.type’ ‘correl.vector’ Argument items with no description in Rd file 'GSEA.Gct2Frame.Rd': ‘filename’ Argument items with no description in Rd file 'GSEA.Gct2Frame2.Rd': ‘filename’ Argument items with no description in Rd file 'GSEA.GeneRanking.Rd': ‘A’ ‘class.labels’ ‘gene.labels’ ‘nperm’ ‘permutation.type’ ‘sigma.correction’ ‘fraction’ ‘replace’ ‘reverse.sign’ Argument items with no description in Rd file 'GSEA.NormalizeCols.Rd': ‘V’ Argument items with no description in Rd file 'GSEA.NormalizeRows.Rd': ‘V’ Argument items with no description in Rd file 'GSEA.ReadClsFile.Rd': ‘file’ Argument items with no description in Rd file 'GSEA.Res2Frame.Rd': ‘filename’ Argument items with no description in Rd file 'GSEA.Threshold.Rd': ‘V’ ‘thres’ ‘ceil’ Argument items with no description in Rd file 'GSEA.VarFilter.Rd': ‘V’ ‘fold’ ‘delta’ ‘gene.names’ Argument items with no description in Rd file 'GSEA.write.gct.Rd': ‘gct’ ‘filename’ Argument items with no description in Rd file 'OLD.GSEA.EnrichmentScore.Rd': ‘gene.list’ ‘gene.set’ * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/canceR.Rcheck/00check.log’ for details.
canceR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL canceR ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘canceR’ ... ** using staged installation ** R ** 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 (canceR)
canceR.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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(canceR) Loading required package: tcltk Loading required package: cBioPortalData Loading required package: AnVIL Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: AnVILBase Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following object is masked from 'package:dplyr': count 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 Attaching package: 'BiocGenerics' The following objects are masked from 'package:dplyr': combine, intersect, setdiff, union 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:dplyr': first, rename 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 Attaching package: 'IRanges' The following objects are masked from 'package:dplyr': collapse, desc, slice 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 > > test_check("canceR") getCancerStudies... OK getCaseLists (1/1) ... OK getClinicalData (1/1) ... OK getGeneticProfiles (1/1) ... OK getProfileData (1/1) ... OK [ FAIL 0 | WARN 1 | SKIP 1 | PASS 0 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_funs.R:8:1' [ FAIL 0 | WARN 1 | SKIP 1 | PASS 0 ] > > proc.time() user system elapsed 19.079 7.569 28.544
canceR.Rcheck/canceR-Ex.timings
name | user | system | elapsed | |
GSEA.Analyze.Sets | 0 | 0 | 0 | |
GSEA.ConsPlot | 0 | 0 | 0 | |
GSEA.EnrichmentScore | 0.000 | 0.000 | 0.001 | |
GSEA.EnrichmentScore2 | 0 | 0 | 0 | |
GSEA.Gct2Frame | 0 | 0 | 0 | |
GSEA.Gct2Frame2 | 0.000 | 0.001 | 0.000 | |
GSEA.GeneRanking | 0 | 0 | 0 | |
GSEA.HeatMapPlot | 0 | 0 | 0 | |
GSEA.HeatMapPlot2 | 0 | 0 | 0 | |
GSEA.NormalizeCols | 0.000 | 0.002 | 0.002 | |
GSEA.NormalizeRows | 0 | 0 | 0 | |
GSEA | 0 | 0 | 0 | |
GSEA.ReadClsFile | 0.001 | 0.000 | 0.000 | |
GSEA.Res2Frame | 0.001 | 0.000 | 0.000 | |
GSEA.Threshold | 0.001 | 0.000 | 0.001 | |
GSEA.VarFilter | 0.000 | 0.001 | 0.001 | |
GSEA.write.gct | 0.000 | 0.001 | 0.001 | |
Match_GeneList_MSigDB | 0.000 | 0.000 | 0.002 | |
OLD.GSEA.EnrichmentScore | 0.001 | 0.000 | 0.001 | |
Run.GSEA | 0.001 | 0.000 | 0.001 | |
UnifyRowNames | 0.113 | 0.038 | 0.283 | |
about | 0.001 | 0.000 | 0.000 | |
canceR | 0 | 0 | 0 | |
canceR_Issue | 0 | 0 | 0 | |
canceR_Vignette | 0 | 0 | 0 | |
cbind.na | 0 | 0 | 0 | |
dialogGeneClassifier | 0.000 | 0.000 | 0.001 | |
dialogMetOption | 0.000 | 0.001 | 0.001 | |
dialogMut | 0.000 | 0.001 | 0.001 | |
dialogOptionCircos | 0.000 | 0.001 | 0.002 | |
dialogOptionGSEAlm | 0 | 0 | 0 | |
dialogOptionPhenoTest | 0.001 | 0.000 | 0.001 | |
dialogPlotOption_SkinCor | 0.000 | 0.001 | 0.000 | |
dialogSamplingGSEA | 0.001 | 0.000 | 0.001 | |
dialogSelectFiles_GSEA | 0.000 | 0.001 | 0.000 | |
dialogSpecificMut | 0.000 | 0.001 | 0.000 | |
dialogSummary_GSEA | 0.000 | 0.000 | 0.001 | |
dialoggetGeneListMSigDB | 0 | 0 | 0 | |
displayInTable | 0 | 0 | 0 | |
getCases | 0.050 | 0.026 | 0.105 | |
getCasesGenProfs | 0.044 | 0.029 | 0.103 | |
getCircos | 0.000 | 0.000 | 0.001 | |
getClinicData_MultipleCases | 0.000 | 0.001 | 0.002 | |
getClinicalDataMatrix | 0.001 | 0.000 | 0.001 | |
getCor_ExpCNAMet | 0.000 | 0.000 | 0.001 | |
getFreqMutData | 0.046 | 0.026 | 0.103 | |
getGCTCLSExample | 0.001 | 0.000 | 0.001 | |
getGCT_CLSfiles | 0 | 0 | 0 | |
getGSEAlm_Diseases | 0 | 0 | 0 | |
getGSEAlm_Variables | 0 | 0 | 0 | |
getGenProfs | 0.049 | 0.022 | 0.100 | |
getGeneExpMatrix | 0.001 | 0.000 | 0.001 | |
getGeneList | 0 | 0 | 0 | |
getGeneListExample | 0 | 0 | 0 | |
getGeneListFromMSigDB | 0.001 | 0.000 | 0.002 | |
getGenesClassifier | 0 | 0 | 0 | |
getGenesTree_MultipleCases | 0 | 0 | 0 | |
getGenesTree_SingleCase | 0.000 | 0.000 | 0.001 | |
getInTable | 0 | 0 | 0 | |
getListProfData | 0.001 | 0.000 | 0.000 | |
getMSigDB | 0 | 0 | 0 | |
getMSigDBExample | 0.001 | 0.000 | 0.001 | |
getMSigDBfile | 0 | 0 | 0 | |
getMegaProfData | 0 | 0 | 0 | |
getMetDataMultipleGenes | 0 | 0 | 0 | |
getMutData | 0.001 | 0.000 | 0.000 | |
getPhenoTest | 0.001 | 0.000 | 0.000 | |
getProfData | 0.080 | 0.002 | 0.107 | |
getProfilesDataMultipleGenes | 0.000 | 0.001 | 0.001 | |
getProfilesDataSingleGene | 0.001 | 0.000 | 0.001 | |
getSpecificMut | 0.001 | 0.000 | 0.001 | |
getSummaryGSEA | 0.001 | 0.000 | 0.001 | |
getSurvival | 0 | 0 | 0 | |
getTextWin | 0 | 0 | 0 | |
geteSet | 0 | 0 | 0 | |
modalDialog | 0.001 | 0.000 | 0.001 | |
myGlobalEnv | 0 | 0 | 0 | |
plotModel | 0.001 | 0.000 | 0.000 | |
plot_1Gene_2GenProfs | 0.001 | 0.000 | 0.001 | |
plot_2Genes_1GenProf | 0.000 | 0.000 | 0.001 | |
rbind.na | 0 | 0 | 0 | |
setWorkspace | 0.001 | 0.000 | 0.001 | |
testCheckedCaseGenProf | 0.000 | 0.000 | 0.001 | |