Kent Riemondy
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/clustifyr |
| git_branch: RELEASE_3_18 |
| git_last_commit: de3d2df |
| git_last_commit_date: 2023-10-24 11:19:27 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:35:51 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 375/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| clustifyr 1.14.0 (landing page) Kent Riemondy
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.14.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings clustifyr_1.14.0.tar.gz |
| StartedAt: 2024-04-15 21:20:27 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 21:31:56 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 689.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: clustifyr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings clustifyr_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/clustifyr.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘clustifyr/DESCRIPTION’ ... OK
* this is package ‘clustifyr’ version ‘1.14.0’
* 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 ... 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 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 ... NOTE
gmt_to_list: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
read.csv
Consider adding
importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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 14.703 0.320 15.025
calculate_pathway_gsea 12.981 0.244 13.233
* 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 ...
‘clustifyr.Rmd’ using ‘UTF-8’... OK
‘geo-annotations.Rmd’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/clustifyr.Rcheck/00check.log’
for details.
clustifyr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL clustifyr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
426.530 7.131 433.673
clustifyr.Rcheck/clustifyr-Ex.timings
| name | user | system | elapsed | |
| append_genes | 0.029 | 0.008 | 0.038 | |
| assess_rank_bias | 0.000 | 0.000 | 0.001 | |
| average_clusters | 0.142 | 0.020 | 0.162 | |
| binarize_expr | 0.625 | 0.032 | 0.657 | |
| build_atlas | 0.057 | 0.012 | 0.069 | |
| calc_distance | 0.004 | 0.000 | 0.004 | |
| calculate_pathway_gsea | 12.981 | 0.244 | 13.233 | |
| call_consensus | 0.185 | 0.004 | 0.190 | |
| call_to_metadata | 0.132 | 0.032 | 0.165 | |
| check_raw_counts | 0.583 | 0.044 | 0.627 | |
| clustify | 0.131 | 0.000 | 0.131 | |
| clustify_lists | 0.062 | 0.004 | 0.067 | |
| clustify_nudge | 0.415 | 0.000 | 0.415 | |
| clustifyr_methods | 0 | 0 | 0 | |
| collapse_to_cluster | 0.560 | 0.048 | 0.608 | |
| compare_lists | 0.654 | 0.072 | 0.726 | |
| cor_to_call | 0.052 | 0.000 | 0.052 | |
| cor_to_call_rank | 0.057 | 0.000 | 0.056 | |
| cor_to_call_topn | 0.059 | 0.000 | 0.059 | |
| downsample_matrix | 0.027 | 0.000 | 0.027 | |
| feature_select_PCA | 0.008 | 0.000 | 0.007 | |
| file_marker_parse | 0.002 | 0.000 | 0.002 | |
| find_rank_bias | 0.031 | 0.000 | 0.031 | |
| gene_pct_markerm | 0.272 | 0.000 | 0.272 | |
| get_ucsc_reference | 0 | 0 | 0 | |
| get_vargenes | 0.000 | 0.000 | 0.001 | |
| gmt_to_list | 0.038 | 0.000 | 0.038 | |
| insert_meta_object | 0 | 0 | 0 | |
| make_comb_ref | 0.007 | 0.011 | 0.019 | |
| marker_select | 0.019 | 0.000 | 0.018 | |
| matrixize_markers | 0.024 | 0.000 | 0.025 | |
| object_data | 0.026 | 0.008 | 0.034 | |
| object_ref | 0.004 | 0.000 | 0.004 | |
| overcluster | 0.858 | 0.044 | 0.902 | |
| overcluster_test | 1.173 | 0.016 | 1.188 | |
| parse_loc_object | 0.001 | 0.000 | 0.001 | |
| plot_best_call | 0.485 | 0.020 | 0.505 | |
| plot_cor | 0.562 | 0.008 | 0.570 | |
| plot_cor_heatmap | 0.807 | 0.008 | 0.816 | |
| plot_dims | 0.237 | 0.000 | 0.236 | |
| plot_gene | 0.454 | 0.004 | 0.458 | |
| plot_pathway_gsea | 14.703 | 0.320 | 15.025 | |
| plot_rank_bias | 0 | 0 | 0 | |
| pos_neg_marker | 0.008 | 0.000 | 0.007 | |
| pos_neg_select | 0.07 | 0.00 | 0.07 | |
| query_rank_bias | 0.038 | 0.000 | 0.038 | |
| ref_feature_select | 0.035 | 0.001 | 0.036 | |
| ref_marker_select | 0.154 | 0.018 | 0.173 | |
| reverse_marker_matrix | 0.003 | 0.000 | 0.004 | |
| run_clustifyr_app | 0 | 0 | 0 | |
| seurat_meta | 0 | 0 | 0 | |
| seurat_ref | 0.002 | 0.000 | 0.002 | |
| write_meta | 0.077 | 0.004 | 0.080 | |