Kent Riemondy
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/clustifyr |
| git_branch: RELEASE_3_16 |
| git_last_commit: 768cfde |
| git_last_commit_date: 2022-11-01 11:21:20 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:28 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the clustifyr package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 355/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| clustifyr 1.10.0 (landing page) Kent Riemondy
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: clustifyr |
| Version: 1.10.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clustifyr.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings clustifyr_1.10.0.tar.gz |
| StartedAt: 2023-04-11 00:05:14 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 00:11:03 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 348.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: clustifyr.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clustifyr.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings clustifyr_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/clustifyr.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'clustifyr/DESCRIPTION' ... OK * this is package 'clustifyr' version '1.10.0' * 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 whether package 'clustifyr' 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 R 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 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
clustifyr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL clustifyr ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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")
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[ FAIL 0 | WARN 7 | SKIP 0 | PASS 176 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 176 ]
>
> proc.time()
user system elapsed
130.81 4.28 139.28
clustifyr.Rcheck/clustifyr-Ex.timings
| name | user | system | elapsed | |
| append_genes | 0.04 | 0.00 | 0.04 | |
| assess_rank_bias | 0 | 0 | 0 | |
| average_clusters | 0.09 | 0.01 | 0.11 | |
| binarize_expr | 0.14 | 0.00 | 0.14 | |
| build_atlas | 0.68 | 0.02 | 0.69 | |
| calc_distance | 0 | 0 | 0 | |
| calculate_pathway_gsea | 3.12 | 0.04 | 3.19 | |
| call_consensus | 0.31 | 0.00 | 0.31 | |
| call_to_metadata | 0.24 | 0.11 | 0.35 | |
| check_raw_counts | 1.47 | 0.01 | 1.48 | |
| clustify | 0.22 | 0.02 | 0.24 | |
| clustify_lists | 0.09 | 0.00 | 0.09 | |
| clustify_nudge | 0.59 | 0.00 | 0.59 | |
| clustifyr_methods | 0 | 0 | 0 | |
| collapse_to_cluster | 1.24 | 0.06 | 1.30 | |
| compare_lists | 0.17 | 0.02 | 0.19 | |
| cor_to_call | 0.08 | 0.00 | 0.08 | |
| cor_to_call_rank | 0.08 | 0.00 | 0.08 | |
| cor_to_call_topn | 0.11 | 0.00 | 0.11 | |
| downsample_matrix | 0.14 | 0.00 | 0.14 | |
| feature_select_PCA | 0.02 | 0.00 | 0.02 | |
| file_marker_parse | 0 | 0 | 0 | |
| find_rank_bias | 0.06 | 0.00 | 0.06 | |
| gene_pct_markerm | 0.41 | 0.00 | 0.40 | |
| get_ucsc_reference | 0 | 0 | 0 | |
| get_vargenes | 0 | 0 | 0 | |
| gmt_to_list | 0.34 | 0.03 | 0.38 | |
| insert_meta_object | 0 | 0 | 0 | |
| make_comb_ref | 0.01 | 0.00 | 0.01 | |
| marker_select | 0.02 | 0.00 | 0.02 | |
| matrixize_markers | 0.03 | 0.01 | 0.05 | |
| object_data | 0.02 | 0.02 | 0.03 | |
| object_ref | 0.01 | 0.00 | 0.01 | |
| overcluster | 1.75 | 0.03 | 1.79 | |
| overcluster_test | 1.49 | 0.06 | 1.54 | |
| parse_loc_object | 0 | 0 | 0 | |
| plot_best_call | 0.78 | 0.04 | 0.81 | |
| plot_cor | 0.68 | 0.00 | 0.67 | |
| plot_cor_heatmap | 0.95 | 0.07 | 1.05 | |
| plot_dims | 0.31 | 0.00 | 0.31 | |
| plot_gene | 0.56 | 0.02 | 0.58 | |
| plot_pathway_gsea | 4.39 | 0.01 | 4.42 | |
| plot_rank_bias | 0 | 0 | 0 | |
| pos_neg_marker | 0 | 0 | 0 | |
| pos_neg_select | 0.05 | 0.02 | 0.06 | |
| query_rank_bias | 0.05 | 0.00 | 0.05 | |
| ref_feature_select | 0.06 | 0.00 | 0.06 | |
| ref_marker_select | 0.19 | 0.01 | 0.20 | |
| reverse_marker_matrix | 0 | 0 | 0 | |
| run_clustifyr_app | 0 | 0 | 0 | |
| seurat_meta | 0 | 0 | 0 | |
| seurat_ref | 0 | 0 | 0 | |
| write_meta | 0.09 | 0.00 | 0.09 | |