Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:40 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 2114/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tidySingleCellExperiment 1.15.1 (landing page) Stefano Mangiola
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the tidySingleCellExperiment package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tidySingleCellExperiment.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: tidySingleCellExperiment |
Version: 1.15.1 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tidySingleCellExperiment.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tidySingleCellExperiment_1.15.1.tar.gz |
StartedAt: 2024-08-27 04:39:43 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 04:44:18 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 275.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tidySingleCellExperiment.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tidySingleCellExperiment.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tidySingleCellExperiment_1.15.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/tidySingleCellExperiment.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘tidySingleCellExperiment/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tidySingleCellExperiment’ version ‘1.15.1’ * 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 ‘tidySingleCellExperiment’ 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 whether startup messages can be suppressed ... 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 ... NOTE select_helper: no visible global function definition for ‘all_of’ aggregate_cells,SingleCellExperiment: no visible binding for global variable ‘my_id_to_split_by___’ aggregate_cells,SingleCellExperiment: no visible binding for global variable ‘assay_name’ aggregate_cells,SingleCellExperiment: no visible binding for global variable ‘.feature’ aggregate_cells,SingleCellExperiment: no visible global function definition for ‘rowData<-’ aggregate_cells,SingleCellExperiment: no visible global function definition for ‘rowData’ Undefined global functions or variables: .feature all_of assay_name my_id_to_split_by___ rowData rowData<- * checking Rd files ... NOTE prepare_Rd: group_by.Rd:98-100: Dropping empty section \seealso * 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 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/tidySingleCellExperiment.Rcheck/00check.log’ for details.
tidySingleCellExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL tidySingleCellExperiment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘tidySingleCellExperiment’ ... ** 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 (tidySingleCellExperiment)
tidySingleCellExperiment.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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(tidySingleCellExperiment) 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 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 > > test_check("tidySingleCellExperiment") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 165 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 165 ] > > proc.time() user system elapsed 29.160 1.157 30.307
tidySingleCellExperiment.Rcheck/tidySingleCellExperiment-Ex.timings
name | user | system | elapsed | |
aggregate_cells | 0.386 | 0.044 | 0.429 | |
arrange | 0.399 | 0.000 | 0.400 | |
as_tibble | 0.139 | 0.004 | 0.144 | |
bind_rows | 0.702 | 0.044 | 0.746 | |
count | 0.123 | 0.000 | 0.123 | |
distinct | 0.117 | 0.000 | 0.116 | |
extract | 0.3 | 0.0 | 0.3 | |
filter | 0.274 | 0.000 | 0.274 | |
formatting | 0.135 | 0.016 | 0.150 | |
full_join | 0.176 | 0.000 | 0.176 | |
ggplot | 0.351 | 0.008 | 0.359 | |
glimpse | 0.024 | 0.000 | 0.024 | |
group_by | 0.156 | 0.000 | 0.157 | |
group_split | 0.462 | 0.012 | 0.474 | |
inner_join | 0.463 | 0.000 | 0.463 | |
join_features | 0.178 | 0.000 | 0.178 | |
join_transcripts | 0 | 0 | 0 | |
left_join | 0.864 | 0.039 | 0.905 | |
mutate | 0.352 | 0.020 | 0.371 | |
nest | 1.210 | 0.008 | 1.218 | |
pipe | 0.000 | 0.000 | 0.001 | |
pivot_longer | 0.183 | 0.000 | 0.182 | |
plot_ly | 0.218 | 0.016 | 0.234 | |
pull | 0.113 | 0.000 | 0.114 | |
rename | 0.394 | 0.008 | 0.401 | |
right_join | 0.464 | 0.000 | 0.464 | |
rowwise | 0 | 0 | 0 | |
sample_n | 0.463 | 0.000 | 0.462 | |
select | 0.302 | 0.000 | 0.302 | |
separate | 1.221 | 0.092 | 1.314 | |
slice | 1.990 | 0.008 | 1.999 | |
summarise | 0.119 | 0.000 | 0.120 | |
tbl_format_header | 0 | 0 | 0 | |
tidy | 0.145 | 0.000 | 0.145 | |
unite | 0.350 | 0.000 | 0.351 | |
unnest | 1.117 | 0.020 | 1.136 | |