Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 381/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
clustifyr 1.18.0 (landing page) Rui Fu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | 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: 1.18.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings clustifyr_1.18.0.tar.gz |
StartedAt: 2024-12-19 21:40:19 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 21:54:17 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 837.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: clustifyr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings clustifyr_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/clustifyr.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘clustifyr/DESCRIPTION’ ... OK * this is package ‘clustifyr’ version ‘1.18.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 14.174 0.195 14.370 calculate_pathway_gsea 12.172 0.230 12.402 * 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 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/clustifyr.Rcheck/00check.log’ for details.
clustifyr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL clustifyr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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(clustifyr) > > test_check("clustifyr") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 183 ] > > proc.time() user system elapsed 367.909 6.010 373.915
clustifyr.Rcheck/clustifyr-Ex.timings
name | user | system | elapsed | |
append_genes | 0.081 | 0.006 | 0.087 | |
assess_rank_bias | 0 | 0 | 0 | |
average_clusters | 0.584 | 0.007 | 0.591 | |
binarize_expr | 0.034 | 0.005 | 0.039 | |
build_atlas | 0.047 | 0.019 | 0.066 | |
calc_distance | 0.004 | 0.000 | 0.004 | |
calculate_pathway_gsea | 12.172 | 0.230 | 12.402 | |
call_consensus | 0.172 | 0.016 | 0.189 | |
call_to_metadata | 0.102 | 0.036 | 0.138 | |
check_raw_counts | 0.601 | 0.042 | 0.643 | |
clustify | 1.087 | 0.068 | 1.155 | |
clustify_lists | 0.583 | 0.016 | 0.599 | |
clustify_nudge | 0.729 | 0.022 | 0.751 | |
clustifyr_methods | 0 | 0 | 0 | |
collapse_to_cluster | 0.535 | 0.033 | 0.567 | |
compare_lists | 0.114 | 0.005 | 0.119 | |
cor_to_call | 0.046 | 0.000 | 0.047 | |
cor_to_call_rank | 0.065 | 0.008 | 0.074 | |
cor_to_call_topn | 0.052 | 0.000 | 0.052 | |
downsample_matrix | 0.01 | 0.00 | 0.01 | |
feature_select_PCA | 0.008 | 0.000 | 0.008 | |
file_marker_parse | 0.002 | 0.000 | 0.002 | |
find_rank_bias | 0.027 | 0.000 | 0.027 | |
gene_pct_markerm | 0.219 | 0.000 | 0.219 | |
get_ucsc_reference | 0 | 0 | 0 | |
get_vargenes | 0.001 | 0.000 | 0.000 | |
gmt_to_list | 0.034 | 0.001 | 0.035 | |
insert_meta_object | 0.188 | 0.000 | 0.188 | |
make_comb_ref | 0.012 | 0.000 | 0.012 | |
marker_select | 0.012 | 0.000 | 0.012 | |
matrixize_markers | 0.020 | 0.001 | 0.022 | |
object_data | 0.260 | 0.001 | 0.261 | |
object_ref | 0.221 | 0.018 | 0.240 | |
overcluster | 1.423 | 0.006 | 1.430 | |
overcluster_test | 0.986 | 0.008 | 0.993 | |
parse_loc_object | 0.186 | 0.042 | 0.226 | |
plot_best_call | 0.474 | 0.015 | 0.490 | |
plot_cor | 0.530 | 0.003 | 0.532 | |
plot_cor_heatmap | 0.739 | 0.005 | 0.746 | |
plot_dims | 0.209 | 0.001 | 0.211 | |
plot_gene | 0.420 | 0.002 | 0.420 | |
plot_pathway_gsea | 14.174 | 0.195 | 14.370 | |
plot_rank_bias | 0.001 | 0.000 | 0.000 | |
pos_neg_marker | 0.006 | 0.001 | 0.007 | |
pos_neg_select | 0.056 | 0.002 | 0.058 | |
query_rank_bias | 0.028 | 0.003 | 0.032 | |
ref_feature_select | 0.023 | 0.001 | 0.025 | |
ref_marker_select | 0.139 | 0.001 | 0.139 | |
reverse_marker_matrix | 0.002 | 0.001 | 0.003 | |
run_clustifyr_app | 0 | 0 | 0 | |
seurat_meta | 0.186 | 0.011 | 0.197 | |
seurat_ref | 0.214 | 0.003 | 0.216 | |
write_meta | 0.231 | 0.004 | 0.234 | |