Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-04 12:05 -0400 (Sat, 04 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 232/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
blase 0.99.3 (landing page) Andrew McCluskey
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | NA | NA | NA | ||||||||||
To the developers/maintainers of the blase package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/blase.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: blase |
Version: 0.99.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:blase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings blase_0.99.3.tar.gz |
StartedAt: 2025-10-03 18:28:51 -0400 (Fri, 03 Oct 2025) |
EndedAt: 2025-10-03 18:31:37 -0400 (Fri, 03 Oct 2025) |
EllapsedTime: 166.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: blase.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:blase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings blase_0.99.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/blase.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘blase/DESCRIPTION’ ... OK * this is package ‘blase’ version ‘0.99.3’ * 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 ‘blase’ can be installed ... OK * checking installed package size ... INFO installed size is 5.2Mb sub-directories of 1Mb or more: data 4.6Mb * 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 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 ... NOTE Non-topic package-anchored link(s) in Rd file 'plot_mapping_result.Rd': ‘[scater:plot_reddim]{scater::plotUMAP()}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed smooth_gene 5.136 0.206 5.351 calculate_gene_peakedness 5.037 0.200 5.241 plot_gene_peakedness 4.969 0.204 5.199 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.22-bioc/meat/blase.Rcheck/00check.log’ for details.
blase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL blase ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘blase’ ... ** this is package ‘blase’ version ‘0.99.3’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (blase)
blase.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(blase) > > test_check("blase") [ FAIL 0 | WARN 4 | SKIP 0 | PASS 124 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 124 ] > > proc.time() user system elapsed 21.164 0.633 21.857
blase.Rcheck/blase-Ex.timings
name | user | system | elapsed | |
BlaseData-class | 0.477 | 0.003 | 0.481 | |
MappingResult | 0.707 | 0.026 | 0.733 | |
annotate_sce | 0.404 | 0.003 | 0.406 | |
as.BlaseData | 0.052 | 0.001 | 0.052 | |
assign_pseudotime_bins | 0.668 | 0.004 | 0.672 | |
bins-getter | 0.053 | 0.000 | 0.054 | |
calculate_gene_peakedness | 5.037 | 0.200 | 5.241 | |
evaluate_parameters | 2.916 | 0.026 | 2.951 | |
evaluate_top_n_genes | 0.890 | 0.004 | 0.893 | |
find_best_params | 1.508 | 0.020 | 1.529 | |
gene_peakedness_spread_selection | 4.771 | 0.226 | 4.998 | |
genes-getter | 0.050 | 0.000 | 0.051 | |
genes-setter | 0.049 | 0.001 | 0.050 | |
get_bins_as_bulk | 0.417 | 0.012 | 0.429 | |
get_top_n_genes | 0.001 | 0.000 | 0.001 | |
map_all_best_bins | 0.596 | 0.003 | 0.606 | |
map_best_bin | 0.601 | 0.002 | 0.612 | |
mapping-result-best-bin-getter | 0.609 | 0.005 | 0.617 | |
mapping-result-best-correlation-getter | 0.603 | 0.003 | 0.613 | |
mapping-result-bootstrap-iterations-getter | 0.603 | 0.003 | 0.611 | |
mapping-result-bulk-name-getter | 0.615 | 0.003 | 0.619 | |
mapping-result-confident-mapping-getter | 0.615 | 0.003 | 0.618 | |
mapping-result-history-getter | 0.602 | 0.002 | 0.605 | |
mapping-result-top-2-distance-getter | 0.609 | 0.003 | 0.616 | |
plot_bin_population | 0.609 | 0.003 | 0.614 | |
plot_find_best_params_results | 1.110 | 0.016 | 1.128 | |
plot_gene_peakedness | 4.969 | 0.204 | 5.199 | |
plot_mapping_result | 2.324 | 0.017 | 2.353 | |
plot_mapping_result_corr | 0.597 | 0.003 | 0.600 | |
plot_mapping_result_heatmap | 0.608 | 0.003 | 0.617 | |
pseudobulk-bins-getter | 0.051 | 0.001 | 0.052 | |
show-MappingResult-method | 0.596 | 0.002 | 0.600 | |
show_blase_object | 0.052 | 0.000 | 0.055 | |
smooth_gene | 5.136 | 0.206 | 5.351 | |