Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:46 -0500 (Mon, 23 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" | 4372 |
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 374/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
clustifyr 1.19.0 (landing page) Rui Fu
| 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 | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: clustifyr |
Version: 1.19.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings clustifyr_1.19.0.tar.gz |
StartedAt: 2024-12-23 06:28:04 -0000 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 06:43:32 -0000 (Mon, 23 Dec 2024) |
EllapsedTime: 927.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: clustifyr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings clustifyr_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/clustifyr.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘clustifyr/DESCRIPTION’ ... OK * this is package ‘clustifyr’ version ‘1.19.0’ * 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 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 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 21.761 0.156 21.969 calculate_pathway_gsea 19.249 0.155 19.453 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/clustifyr.Rcheck/00check.log’ for details.
clustifyr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL clustifyr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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(clustifyr) > > test_check("clustifyr") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 183 ] > > proc.time() user system elapsed 589.774 8.959 600.099
clustifyr.Rcheck/clustifyr-Ex.timings
name | user | system | elapsed | |
append_genes | 0.133 | 0.000 | 0.133 | |
assess_rank_bias | 0.000 | 0.000 | 0.001 | |
average_clusters | 0.860 | 0.008 | 0.869 | |
binarize_expr | 0.077 | 0.004 | 0.082 | |
build_atlas | 0.115 | 0.008 | 0.123 | |
calc_distance | 0.007 | 0.000 | 0.007 | |
calculate_pathway_gsea | 19.249 | 0.155 | 19.453 | |
call_consensus | 0.276 | 0.024 | 0.300 | |
call_to_metadata | 0.151 | 0.040 | 0.192 | |
check_raw_counts | 1.030 | 0.056 | 1.089 | |
clustify | 2.828 | 0.020 | 2.853 | |
clustify_lists | 0.903 | 0.000 | 0.905 | |
clustify_nudge | 1.837 | 0.040 | 1.882 | |
clustifyr_methods | 0 | 0 | 0 | |
collapse_to_cluster | 2.491 | 0.028 | 2.522 | |
compare_lists | 0.213 | 0.004 | 0.218 | |
cor_to_call | 0.09 | 0.00 | 0.09 | |
cor_to_call_rank | 0.132 | 0.004 | 0.138 | |
cor_to_call_topn | 0.112 | 0.000 | 0.112 | |
downsample_matrix | 0.017 | 0.000 | 0.017 | |
feature_select_PCA | 0.013 | 0.000 | 0.014 | |
file_marker_parse | 0.000 | 0.002 | 0.003 | |
find_rank_bias | 0.059 | 0.002 | 0.060 | |
gene_pct_markerm | 0.643 | 0.012 | 0.656 | |
get_ucsc_reference | 0 | 0 | 0 | |
get_vargenes | 0 | 0 | 0 | |
gmt_to_list | 0.046 | 0.004 | 0.052 | |
insert_meta_object | 0.364 | 0.008 | 0.372 | |
make_comb_ref | 0.033 | 0.003 | 0.036 | |
marker_select | 0.035 | 0.004 | 0.038 | |
matrixize_markers | 0.037 | 0.000 | 0.037 | |
object_data | 0.511 | 0.011 | 0.525 | |
object_ref | 0.438 | 0.020 | 0.459 | |
overcluster | 2.226 | 0.064 | 2.295 | |
overcluster_test | 1.572 | 0.012 | 1.587 | |
parse_loc_object | 0.338 | 0.008 | 0.346 | |
plot_best_call | 0.629 | 0.024 | 0.654 | |
plot_cor | 0.774 | 0.008 | 0.784 | |
plot_cor_heatmap | 1.131 | 0.004 | 1.137 | |
plot_dims | 0.305 | 0.003 | 0.309 | |
plot_gene | 0.580 | 0.004 | 0.586 | |
plot_pathway_gsea | 21.761 | 0.156 | 21.969 | |
plot_rank_bias | 0 | 0 | 0 | |
pos_neg_marker | 0.011 | 0.000 | 0.010 | |
pos_neg_select | 0.112 | 0.004 | 0.116 | |
query_rank_bias | 0.06 | 0.00 | 0.06 | |
ref_feature_select | 0.057 | 0.000 | 0.057 | |
ref_marker_select | 0.248 | 0.000 | 0.248 | |
reverse_marker_matrix | 0.004 | 0.000 | 0.004 | |
run_clustifyr_app | 0 | 0 | 0 | |
seurat_meta | 0.321 | 0.004 | 0.326 | |
seurat_ref | 0.404 | 0.004 | 0.409 | |
write_meta | 0.417 | 0.008 | 0.426 | |