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 11:39 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 153/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Benjamin Schuster-Boeckler
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the BEARscc package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BEARscc.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: BEARscc |
Version: 1.27.1 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BEARscc.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BEARscc_1.27.1.tar.gz |
StartedAt: 2024-12-23 19:58:36 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 20:02:47 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 250.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: BEARscc.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BEARscc.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BEARscc_1.27.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BEARscc.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 ‘BEARscc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BEARscc’ version ‘1.27.1’ * 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 ‘BEARscc’ 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘BEARscc-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: report_cell_metrics > ### Title: Reports BEARscc metrics for cells. > ### Aliases: report_cell_metrics calculate_cell_metrics > ### calculate_cell_metrics_by_cluster . rn > ### Keywords: list > > ### ** Examples > > data(analysis_examples) > > cell_scores.df <- report_cell_metrics(BEARscc_clusts.df, noise_consensus) Error in doWithOneRestart(return(expr), restart) : bad error message Calls: report_cell_metrics ... signal -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed estimate_noiseparameters 6.347 0.227 6.484 * 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: 1 ERROR See ‘/home/biocbuild/bbs-3.21-bioc/meat/BEARscc.Rcheck/00check.log’ for details.
BEARscc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BEARscc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘BEARscc’ ... ** 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 Warning in fun(libname, pkgname) : Package 'BEARscc' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'BEARscc' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package keeps a record of temporary installation path * DONE (BEARscc)
BEARscc.Rcheck/tests/testthat.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. > library(testthat) > library(BEARscc) Warning message: In fun(libname, pkgname) : Package 'BEARscc' is deprecated and will be removed from Bioconductor version 3.22 > > test_check("BEARscc") [1] "Running BEARscc on example data to test for correct installation." [1] "Fitting parameter alpha to establish spike-in derived noise model." [1] "Estimating error for spike-ins with alpha = 0" [1] "Estimating error for spike-ins with alpha = 0.25" [1] "Estimating error for spike-ins with alpha = 0.5" [1] "Estimating error for spike-ins with alpha = 0.75" [1] "Estimating error for spike-ins with alpha = 1" [1] "There are adequate spike-in drop-outs to build the drop-out model. Estimating the drop-out model now." [1] "Injecting noise for testing..." [1] "Creating a simulated replicated counts matrix: 1." [1] "Creating a simulated replicated counts matrix: 2." [1] "Creating a simulated replicated counts matrix: 3." [1] "Creating consensus matrix for testing..." [1] "Computing cluster and cell metrics for testing..." [ FAIL 0 | WARN 13 | SKIP 0 | PASS 25 ] [ FAIL 0 | WARN 13 | SKIP 0 | PASS 25 ] > > proc.time() user system elapsed 16.486 0.713 17.143
BEARscc.Rcheck/BEARscc-Ex.timings
name | user | system | elapsed | |
BEARscc_examples | 0.033 | 0.000 | 0.033 | |
analysis_examples | 0.651 | 0.003 | 0.654 | |
cluster_consensus | 0.042 | 0.004 | 0.046 | |
compute_consensus | 0.070 | 0.015 | 0.085 | |
estimate_noiseparameters | 6.347 | 0.227 | 6.484 | |