Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-28 17:43 -0400 (Fri, 28 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
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 380/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
clustifyr 1.16.0 (landing page) Kent Riemondy
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the clustifyr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clustifyr.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: clustifyr |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clustifyr_1.16.0.tar.gz |
StartedAt: 2024-06-27 02:12:18 -0400 (Thu, 27 Jun 2024) |
EndedAt: 2024-06-27 02:36:21 -0400 (Thu, 27 Jun 2024) |
EllapsedTime: 1443.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: clustifyr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clustifyr_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/clustifyr.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘clustifyr/DESCRIPTION’ ... OK * this is package ‘clustifyr’ version ‘1.16.0’ * 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 ‘clustifyr’ 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 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 LazyData ... 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 plot_pathway_gsea 25.877 0.176 31.379 calculate_pathway_gsea 22.594 0.177 27.519 plot_cor_heatmap 2.119 0.103 6.055 * 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-3.19-bioc/meat/clustifyr.Rcheck/00check.log’ for details.
clustifyr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL clustifyr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘clustifyr’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (clustifyr)
clustifyr.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > library(testthat) > library(clustifyr) > > test_check("clustifyr") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 183 ] > > proc.time() user system elapsed 683.163 10.946 817.821
clustifyr.Rcheck/clustifyr-Ex.timings
name | user | system | elapsed | |
append_genes | 0.071 | 0.014 | 0.104 | |
assess_rank_bias | 0.000 | 0.001 | 0.001 | |
average_clusters | 0.856 | 0.025 | 1.079 | |
binarize_expr | 0.067 | 0.003 | 0.083 | |
build_atlas | 0.096 | 0.019 | 0.149 | |
calc_distance | 0.009 | 0.001 | 0.011 | |
calculate_pathway_gsea | 22.594 | 0.177 | 27.519 | |
call_consensus | 0.418 | 0.015 | 0.513 | |
call_to_metadata | 0.369 | 0.520 | 1.148 | |
check_raw_counts | 0.909 | 0.069 | 1.253 | |
clustify | 3.214 | 0.156 | 4.111 | |
clustify_lists | 0.897 | 0.033 | 1.133 | |
clustify_nudge | 1.866 | 0.052 | 2.299 | |
clustifyr_methods | 0.001 | 0.001 | 0.000 | |
collapse_to_cluster | 1.359 | 0.133 | 1.844 | |
compare_lists | 0.278 | 0.009 | 0.358 | |
cor_to_call | 0.100 | 0.002 | 0.117 | |
cor_to_call_rank | 0.151 | 0.015 | 0.178 | |
cor_to_call_topn | 0.119 | 0.001 | 0.140 | |
downsample_matrix | 0.018 | 0.001 | 0.020 | |
feature_select_PCA | 0.016 | 0.005 | 0.030 | |
file_marker_parse | 0.004 | 0.003 | 0.009 | |
find_rank_bias | 0.075 | 0.004 | 0.098 | |
gene_pct_markerm | 0.570 | 0.007 | 0.693 | |
get_ucsc_reference | 0.000 | 0.001 | 0.001 | |
get_vargenes | 0.001 | 0.001 | 0.004 | |
gmt_to_list | 0.080 | 0.004 | 0.096 | |
insert_meta_object | 0.525 | 0.013 | 0.658 | |
make_comb_ref | 0.030 | 0.002 | 0.038 | |
marker_select | 0.024 | 0.002 | 0.028 | |
matrixize_markers | 0.061 | 0.015 | 0.094 | |
object_data | 0.967 | 0.032 | 1.209 | |
object_ref | 0.672 | 0.305 | 1.195 | |
overcluster | 2.967 | 0.138 | 3.790 | |
overcluster_test | 2.543 | 0.090 | 3.223 | |
parse_loc_object | 0.537 | 0.031 | 0.716 | |
plot_best_call | 0.955 | 0.075 | 1.283 | |
plot_cor | 1.301 | 0.025 | 1.619 | |
plot_cor_heatmap | 2.119 | 0.103 | 6.055 | |
plot_dims | 0.558 | 0.012 | 0.702 | |
plot_gene | 0.971 | 0.034 | 1.240 | |
plot_pathway_gsea | 25.877 | 0.176 | 31.379 | |
plot_rank_bias | 0.001 | 0.002 | 0.002 | |
pos_neg_marker | 0.018 | 0.000 | 0.022 | |
pos_neg_select | 0.236 | 0.004 | 0.292 | |
query_rank_bias | 0.084 | 0.004 | 0.107 | |
ref_feature_select | 0.042 | 0.002 | 0.054 | |
ref_marker_select | 0.544 | 0.004 | 0.673 | |
reverse_marker_matrix | 0.011 | 0.013 | 0.032 | |
run_clustifyr_app | 0.000 | 0.001 | 0.001 | |
seurat_meta | 0.513 | 0.005 | 0.622 | |
seurat_ref | 0.562 | 0.007 | 0.683 | |
write_meta | 0.965 | 0.038 | 1.210 | |