Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:36:37 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 1050/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
iSEE 2.15.0 (landing page) Kevin Rue-Albrecht
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | 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 | ERROR | ||||||||||
To the developers/maintainers of the iSEE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iSEE.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: iSEE |
Version: 2.15.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:iSEE.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings iSEE_2.15.0.tar.gz |
StartedAt: 2024-03-27 23:36:58 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 23:44:01 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 423.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: iSEE.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:iSEE.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings iSEE_2.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/iSEE.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘iSEE/DESCRIPTION’ ... OK * this is package ‘iSEE’ version ‘2.15.0’ * 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 ‘iSEE’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’ 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 ... NOTE checkRd: (-1) registerAppOptions.Rd:46-48: Lost braces in \itemize; meant \describe ? checkRd: (-1) registerAppOptions.Rd:49-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) registerAppOptions.Rd:52-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) registerAppOptions.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) registerAppOptions.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) registerAppOptions.Rd:57: Lost braces in \itemize; meant \describe ? * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed checkColormapCompatibility 11.206 0.812 12.018 synchronizeAssays 7.858 0.508 8.367 iSEE 7.057 0.527 7.586 * 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: 23. │ └─alabaster.se (local) meth(path, metadata = metadata, ...) 24. │ └─alabaster.base::altReadObject(path, metadata = metadata, ...) 25. │ └─scRNAseq (local) FUN(...) 26. │ └─alabaster.base::readObject(...) 27. │ └─alabaster.se (local) meth(path, metadata = metadata, ...) 28. │ └─alabaster.base::altReadObject(...) 29. │ └─scRNAseq (local) FUN(...) 30. │ └─alabaster.base::readObject(...) 31. │ └─alabaster.matrix (local) meth(path, metadata = metadata, ...) 32. │ └─(function() {... 33. │ └─rhdf5::H5Fopen(fpath) 34. └─base::.handleSimpleError(...) 35. └─testthat (local) h(simpleError(msg, call)) 36. └─rlang::abort(...) Execution halted * 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: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/iSEE.Rcheck/00check.log’ for details.
iSEE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL iSEE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘iSEE’ ... ** 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 (iSEE)
iSEE.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 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(iSEE) 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 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, 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 Loading required package: SingleCellExperiment > > test_check("iSEE") Loading required package: scRNAseq Loading required package: scater Loading required package: scuttle Loading required package: ggplot2 Error in `FUN()`: ! In path: "/home/biocbuild/bbs-3.19-bioc/meat/iSEE.Rcheck/tests/testthat/setup_sce.R" Caused by error in `H5Fopen()`: ! HDF5. File accessibility. Unable to open file. Backtrace: ▆ 1. ├─testthat::test_check("iSEE") 2. │ └─testthat::test_dir(...) 3. │ └─testthat:::test_files(...) 4. │ └─testthat:::test_files_serial(...) 5. │ └─testthat:::test_files_setup_state(...) 6. │ └─testthat::source_test_setup(".", env) 7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE) 8. │ └─base::lapply(...) 9. │ └─testthat (local) FUN(X[[i]], ...) 10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap) 11. │ ├─base::withCallingHandlers(...) 12. │ └─base::eval(exprs, env) 13. │ └─base::eval(exprs, env) 14. │ └─scRNAseq::ReprocessedAllenData(assays = "tophat_counts") at tests/testthat/setup_sce.R:7:1 15. │ └─scRNAseq::fetchDataset("legacy", "2023-12-18", "allen", realize.assays = TRUE) 16. │ └─alabaster.base::altReadObject(...) 17. │ └─scRNAseq (local) FUN(...) 18. │ └─alabaster.base::readObject(...) 19. │ └─alabaster.sce (local) meth(path, metadata = metadata, ...) 20. │ └─alabaster.base::altReadObject(path, metadata, ...) 21. │ └─scRNAseq (local) FUN(...) 22. │ └─alabaster.base::readObject(...) 23. │ └─alabaster.se (local) meth(path, metadata = metadata, ...) 24. │ └─alabaster.base::altReadObject(path, metadata = metadata, ...) 25. │ └─scRNAseq (local) FUN(...) 26. │ └─alabaster.base::readObject(...) 27. │ └─alabaster.se (local) meth(path, metadata = metadata, ...) 28. │ └─alabaster.base::altReadObject(...) 29. │ └─scRNAseq (local) FUN(...) 30. │ └─alabaster.base::readObject(...) 31. │ └─alabaster.matrix (local) meth(path, metadata = metadata, ...) 32. │ └─(function() {... 33. │ └─rhdf5::H5Fopen(fpath) 34. └─base::.handleSimpleError(...) 35. └─testthat (local) h(simpleError(msg, call)) 36. └─rlang::abort(...) Execution halted
iSEE.Rcheck/iSEE-Ex.timings
name | user | system | elapsed | |
ColumnDataPlot-class | 2.523 | 0.156 | 2.680 | |
ColumnDataTable-class | 0.453 | 0.076 | 0.529 | |
ComplexHeatmapPlot-class | 0.668 | 0.024 | 0.693 | |
ExperimentColorMap-class | 0.02 | 0.00 | 0.02 | |
FeatureAssayPlot-class | 0.664 | 0.004 | 0.668 | |
ReducedDimensionPlot-class | 0.970 | 0.000 | 0.971 | |
RowDataPlot-class | 0.648 | 0.004 | 0.652 | |
RowDataTable-class | 0.436 | 0.000 | 0.436 | |
SampleAssayPlot-class | 0.634 | 0.028 | 0.661 | |
aes-utils | 0.000 | 0.000 | 0.001 | |
cache-utils | 0.040 | 0.004 | 0.044 | |
checkColormapCompatibility | 11.206 | 0.812 | 12.018 | |
class-utils | 0.003 | 0.000 | 0.002 | |
cleanDataset | 0.049 | 0.004 | 0.053 | |
collapseBox | 0.032 | 0.000 | 0.032 | |
createCustomPanels | 0.069 | 0.010 | 0.079 | |
createLandingPage | 0.119 | 0.007 | 0.128 | |
defaultTour | 0.008 | 0.000 | 0.008 | |
filterDTColumn | 0.000 | 0.004 | 0.004 | |
getPanelColor | 0.156 | 0.031 | 0.187 | |
iSEE | 7.057 | 0.527 | 7.586 | |
iSEEOptions | 0 | 0 | 0 | |
jitterPoints | 0.048 | 0.015 | 0.063 | |
labs-utils | 0.000 | 0.000 | 0.001 | |
lassoPoints | 0.005 | 0.000 | 0.006 | |
manage_commands | 0.000 | 0.000 | 0.001 | |
multiSelectionToFactor | 0.001 | 0.000 | 0.002 | |
panelDefaults | 0.001 | 0.000 | 0.001 | |
plot-utils | 0.008 | 0.004 | 0.012 | |
registerAppOptions | 0.005 | 0.000 | 0.006 | |
selectionColorMap | 0.002 | 0.000 | 0.002 | |
setCachedCommonInfo | 0.003 | 0.000 | 0.004 | |
subsetPointsByGrid | 0.513 | 0.032 | 0.545 | |
synchronizeAssays | 7.858 | 0.508 | 8.367 | |