Kent Riemondy
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/clustifyr |
| git_branch: RELEASE_3_17 |
| git_last_commit: 82ccda3 |
| git_last_commit_date: 2023-04-25 11:15:27 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:16 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 371/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| clustifyr 1.12.0 (landing page) Kent Riemondy
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / 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: 1.12.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings clustifyr_1.12.0.tar.gz |
| StartedAt: 2023-10-15 20:11:16 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 20:22:08 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 651.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: clustifyr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings clustifyr_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/clustifyr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘clustifyr/DESCRIPTION’ ... OK
* this is package ‘clustifyr’ version ‘1.12.0’
* 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 ... 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 16.487 0.164 16.651
calculate_pathway_gsea 13.525 0.268 13.999
* 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
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
clustifyr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL clustifyr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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
405.662 5.265 410.942
clustifyr.Rcheck/clustifyr-Ex.timings
| name | user | system | elapsed | |
| append_genes | 0.035 | 0.020 | 0.054 | |
| assess_rank_bias | 0.000 | 0.001 | 0.000 | |
| average_clusters | 0.087 | 0.008 | 0.096 | |
| binarize_expr | 0.035 | 0.008 | 0.044 | |
| build_atlas | 0.071 | 0.008 | 0.079 | |
| calc_distance | 0.004 | 0.000 | 0.003 | |
| calculate_pathway_gsea | 13.525 | 0.268 | 13.999 | |
| call_consensus | 0.211 | 0.036 | 0.247 | |
| call_to_metadata | 0.129 | 0.204 | 0.333 | |
| check_raw_counts | 0.719 | 0.040 | 0.759 | |
| clustify | 0.155 | 0.015 | 0.170 | |
| clustify_lists | 0.067 | 0.004 | 0.070 | |
| clustify_nudge | 0.437 | 0.028 | 0.465 | |
| clustifyr_methods | 0 | 0 | 0 | |
| collapse_to_cluster | 1.334 | 0.108 | 1.442 | |
| compare_lists | 0.124 | 0.000 | 0.125 | |
| cor_to_call | 0.058 | 0.000 | 0.058 | |
| cor_to_call_rank | 0.064 | 0.000 | 0.064 | |
| cor_to_call_topn | 0.076 | 0.000 | 0.076 | |
| downsample_matrix | 0.052 | 0.000 | 0.052 | |
| feature_select_PCA | 0.013 | 0.000 | 0.013 | |
| file_marker_parse | 0.003 | 0.000 | 0.006 | |
| find_rank_bias | 0.046 | 0.004 | 0.061 | |
| gene_pct_markerm | 0.405 | 0.012 | 0.418 | |
| get_ucsc_reference | 0 | 0 | 0 | |
| get_vargenes | 0.001 | 0.000 | 0.001 | |
| gmt_to_list | 0.299 | 0.005 | 0.324 | |
| insert_meta_object | 0 | 0 | 0 | |
| make_comb_ref | 0.013 | 0.000 | 0.013 | |
| marker_select | 0.016 | 0.000 | 0.016 | |
| matrixize_markers | 0.032 | 0.003 | 0.036 | |
| object_data | 0.038 | 0.000 | 0.038 | |
| object_ref | 0.000 | 0.007 | 0.008 | |
| overcluster | 1.532 | 0.108 | 1.640 | |
| overcluster_test | 1.129 | 0.023 | 1.152 | |
| parse_loc_object | 0.001 | 0.000 | 0.001 | |
| plot_best_call | 0.545 | 0.004 | 0.549 | |
| plot_cor | 0.557 | 0.023 | 0.581 | |
| plot_cor_heatmap | 0.840 | 0.036 | 0.875 | |
| plot_dims | 0.297 | 0.000 | 0.297 | |
| plot_gene | 0.504 | 0.000 | 0.505 | |
| plot_pathway_gsea | 16.487 | 0.164 | 16.651 | |
| plot_rank_bias | 0.000 | 0.000 | 0.001 | |
| pos_neg_marker | 0.008 | 0.001 | 0.008 | |
| pos_neg_select | 0.080 | 0.004 | 0.084 | |
| query_rank_bias | 0.033 | 0.003 | 0.036 | |
| ref_feature_select | 0.031 | 0.001 | 0.031 | |
| ref_marker_select | 0.152 | 0.000 | 0.152 | |
| reverse_marker_matrix | 0.006 | 0.000 | 0.006 | |
| run_clustifyr_app | 0.001 | 0.000 | 0.001 | |
| seurat_meta | 0.000 | 0.000 | 0.001 | |
| seurat_ref | 0.000 | 0.002 | 0.002 | |
| write_meta | 0.074 | 0.000 | 0.075 | |