Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 2113/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TENxIO 1.9.3 (landing page) Marcel Ramos
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the TENxIO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TENxIO.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: TENxIO |
Version: 1.9.3 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:TENxIO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings TENxIO_1.9.3.tar.gz |
StartedAt: 2024-12-24 02:50:20 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 02:53:33 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 193.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TENxIO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:TENxIO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings TENxIO_1.9.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/TENxIO.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘TENxIO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TENxIO’ version ‘1.9.3’ * 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 ‘TENxIO’ 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 ... OK * checking Rd contents ... OK * 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 ‘tinytest.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: OK
TENxIO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL TENxIO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘TENxIO’ ... ** 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 (TENxIO)
TENxIO.Rcheck/tests/tinytest.Rout
R Under development (unstable) (2024-10-21 r87258) -- "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. > if (requireNamespace("tinytest", quietly = TRUE)) + tinytest::test_package("TENxIO") Loading required package: SingleCellExperiment 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: 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_TENxFile-class.R......... 1 tests [0;32mOK[0m test_TENxFile-class.R......... 1 tests [0;32mOK[0m test_TENxFile-class.R......... 1 tests [0;32mOK[0m test_TENxFile-class.R......... 2 tests [0;32mOK[0m test_TENxFile-class.R......... 2 tests [0;32mOK[0m test_TENxFile-class.R......... 3 tests [0;32mOK[0m test_TENxFile-class.R......... 3 tests [0;32mOK[0m test_TENxFile-class.R......... 3 tests [0;32mOK[0m test_TENxFile-class.R......... 3 tests [0;32mOK[0m test_TENxFile-class.R......... 4 tests [0;32mOK[0m test_TENxFile-class.R......... 5 tests [0;32mOK[0m test_TENxFile-class.R......... 6 tests [0;32mOK[0m test_TENxFile-class.R......... 6 tests [0;32mOK[0m test_TENxFile-class.R......... 6 tests [0;32mOK[0m test_TENxFile-class.R......... 6 tests [0;32mOK[0m test_TENxFile-class.R......... 6 tests [0;32mOK[0m test_TENxFile-class.R......... 7 tests [0;32mOK[0m test_TENxFile-class.R......... 7 tests [0;32mOK[0m test_TENxFile-class.R......... 7 tests [0;32mOK[0m test_TENxFile-class.R......... 9 tests [0;32mOK[0m [0;34m1.0s[0m test_TENxFileList-class.R..... 0 tests test_TENxFileList-class.R..... 0 tests test_TENxFileList-class.R..... 1 tests [0;32mOK[0m test_TENxFileList-class.R..... 2 tests [0;32mOK[0m test_TENxFileList-class.R..... 3 tests [0;32mOK[0m test_TENxFileList-class.R..... 3 tests [0;32mOK[0m test_TENxFileList-class.R..... 4 tests [0;32mOK[0m test_TENxFileList-class.R..... 5 tests [0;32mOK[0m test_TENxFileList-class.R..... 6 tests [0;32mOK[0m test_TENxFileList-class.R..... 7 tests [0;32mOK[0m test_TENxFileList-class.R..... 8 tests [0;32mOK[0m test_TENxFileList-class.R..... 9 tests [0;32mOK[0m [0;34m1.2s[0m test_TENxFragments-class.R.... 0 tests test_TENxFragments-class.R.... 1 tests [0;32mOK[0m test_TENxFragments-class.R.... 1 tests [0;32mOK[0m test_TENxFragments-class.R.... 2 tests [0;32mOK[0m test_TENxFragments-class.R.... 3 tests [0;32mOK[0m test_TENxFragments-class.R.... 4 tests [0;32mOK[0m test_TENxFragments-class.R.... 4 tests [0;32mOK[0m test_TENxFragments-class.R.... 5 tests [0;32mOK[0m test_TENxFragments-class.R.... 6 tests [0;32mOK[0m test_TENxFragments-class.R.... 7 tests [0;32mOK[0m [0;34m1.0s[0m test_TENxH5-class.R........... 0 tests test_TENxH5-class.R........... 0 tests test_TENxH5-class.R........... 1 tests [0;32mOK[0m test_TENxH5-class.R........... 2 tests [0;32mOK[0m test_TENxH5-class.R........... 2 tests [0;32mOK[0m test_TENxH5-class.R........... 3 tests [0;32mOK[0m test_TENxH5-class.R........... 4 tests [0;32mOK[0m test_TENxH5-class.R........... 4 tests [0;32mOK[0m preview <= 12 rowRanges: pbmc_granulocyte_ff_bc_ex.h5 test_TENxH5-class.R........... 4 tests [0;32mOK[0m test_TENxH5-class.R........... 5 tests [0;32mOK[0m test_TENxH5-class.R........... 6 tests [0;32mOK[0m test_TENxH5-class.R........... 7 tests [0;32mOK[0m test_TENxH5-class.R........... 8 tests [0;32mOK[0m test_TENxH5-class.R........... 9 tests [0;32mOK[0m [0;34m0.8s[0m test_TENxMTX-class.R.......... 0 tests test_TENxMTX-class.R.......... 0 tests test_TENxMTX-class.R.......... 1 tests [0;32mOK[0m test_TENxMTX-class.R.......... 2 tests [0;32mOK[0m test_TENxMTX-class.R.......... 3 tests [0;32mOK[0m test_TENxMTX-class.R.......... 3 tests [0;32mOK[0m test_TENxMTX-class.R.......... 4 tests [0;32mOK[0m test_TENxMTX-class.R.......... 5 tests [0;32mOK[0m test_TENxMTX-class.R.......... 6 tests [0;32mOK[0m [0;36m24ms[0m test_TENxPeaks-class.R........ 0 tests test_TENxPeaks-class.R........ 0 tests test_TENxPeaks-class.R........ 1 tests [0;32mOK[0m test_TENxPeaks-class.R........ 2 tests [0;32mOK[0m test_TENxPeaks-class.R........ 2 tests [0;32mOK[0m test_TENxPeaks-class.R........ 3 tests [0;32mOK[0m test_TENxPeaks-class.R........ 4 tests [0;32mOK[0m test_TENxPeaks-class.R........ 5 tests [0;32mOK[0m test_TENxPeaks-class.R........ 5 tests [0;32mOK[0m test_TENxPeaks-class.R........ 6 tests [0;32mOK[0m test_TENxPeaks-class.R........ 7 tests [0;32mOK[0m test_TENxPeaks-class.R........ 8 tests [0;32mOK[0m test_TENxPeaks-class.R........ 9 tests [0;32mOK[0m test_TENxPeaks-class.R........ 10 tests [0;32mOK[0m test_TENxPeaks-class.R........ 11 tests [0;32mOK[0m test_TENxPeaks-class.R........ 12 tests [0;32mOK[0m test_TENxPeaks-class.R........ 13 tests [0;32mOK[0m test_TENxPeaks-class.R........ 14 tests [0;32mOK[0m [0;34m0.2s[0m All ok, 54 results (4.2s) Warning messages: 1: In rhdf5::h5read(file, name = paste0(group, ranges), index = list(1L), : Object 'matrix/features/interval' does not exist in this HDF5 file. 2: In TENxFragments(fr, extension = "tsv.gz") : Using default 'yieldSize' parameter > > proc.time() user system elapsed 10.414 0.616 11.521
TENxIO.Rcheck/TENxIO-Ex.timings
name | user | system | elapsed | |
TENxFile | 0.000 | 0.000 | 0.001 | |
TENxFileList | 0.984 | 0.185 | 1.170 | |
TENxFragments | 1.113 | 0.019 | 1.133 | |
TENxH5 | 1.933 | 0.046 | 1.980 | |
TENxMTX | 0.019 | 0.001 | 0.020 | |
TENxPeaks | 1.134 | 0.067 | 1.199 | |