| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:14:56 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 351/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| clustifyr 1.11.1 (landing page) Kent Riemondy
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: clustifyr |
| Version: 1.11.1 |
| 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/library --timings clustifyr_1.11.1.tar.gz |
| StartedAt: 2023-02-06 21:26:50 -0000 (Mon, 06 Feb 2023) |
| EndedAt: 2023-02-06 21:43:06 -0000 (Mon, 06 Feb 2023) |
| EllapsedTime: 976.6 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/library --timings clustifyr_1.11.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/clustifyr.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘clustifyr/DESCRIPTION’ ... OK
* this is package ‘clustifyr’ version ‘1.11.1’
* 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 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 19.411 0.020 23.140
calculate_pathway_gsea 15.395 0.008 23.746
collapse_to_cluster 3.549 0.033 5.777
* 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/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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
527.506 2.300 597.810
clustifyr.Rcheck/clustifyr-Ex.timings
| name | user | system | elapsed | |
| append_genes | 0.684 | 0.012 | 1.402 | |
| assess_rank_bias | 0 | 0 | 0 | |
| average_clusters | 0.107 | 0.004 | 0.230 | |
| binarize_expr | 0.087 | 0.000 | 0.091 | |
| build_atlas | 0.134 | 0.008 | 0.152 | |
| calc_distance | 0.004 | 0.000 | 0.005 | |
| calculate_pathway_gsea | 15.395 | 0.008 | 23.746 | |
| call_consensus | 0.329 | 0.003 | 0.558 | |
| call_to_metadata | 0.160 | 0.087 | 0.414 | |
| check_raw_counts | 0.834 | 0.031 | 1.558 | |
| clustify | 0.277 | 0.000 | 0.343 | |
| clustify_lists | 0.106 | 0.004 | 0.133 | |
| clustify_nudge | 1.076 | 0.011 | 1.523 | |
| clustifyr_methods | 0.001 | 0.000 | 0.001 | |
| collapse_to_cluster | 3.549 | 0.033 | 5.777 | |
| compare_lists | 0.187 | 0.000 | 0.223 | |
| cor_to_call | 0.103 | 0.000 | 0.103 | |
| cor_to_call_rank | 0.112 | 0.000 | 0.113 | |
| cor_to_call_topn | 0.115 | 0.000 | 0.115 | |
| downsample_matrix | 0.112 | 0.003 | 0.120 | |
| feature_select_PCA | 0.014 | 0.000 | 0.017 | |
| file_marker_parse | 0.002 | 0.000 | 0.003 | |
| find_rank_bias | 0.092 | 0.000 | 0.093 | |
| gene_pct_markerm | 0.820 | 0.000 | 0.861 | |
| get_ucsc_reference | 0 | 0 | 0 | |
| get_vargenes | 0.001 | 0.000 | 0.001 | |
| gmt_to_list | 0.412 | 0.012 | 0.531 | |
| insert_meta_object | 0.000 | 0.000 | 0.001 | |
| make_comb_ref | 0.036 | 0.000 | 0.065 | |
| marker_select | 0.051 | 0.000 | 0.090 | |
| matrixize_markers | 0.033 | 0.016 | 0.053 | |
| object_data | 0.059 | 0.004 | 0.108 | |
| object_ref | 0.006 | 0.000 | 0.006 | |
| overcluster | 3.883 | 0.054 | 4.388 | |
| overcluster_test | 1.617 | 0.011 | 2.184 | |
| parse_loc_object | 0.000 | 0.000 | 0.007 | |
| plot_best_call | 0.753 | 0.016 | 1.114 | |
| plot_cor | 0.718 | 0.015 | 1.250 | |
| plot_cor_heatmap | 1.177 | 0.020 | 1.933 | |
| plot_dims | 0.438 | 0.004 | 0.838 | |
| plot_gene | 0.622 | 0.008 | 0.865 | |
| plot_pathway_gsea | 19.411 | 0.020 | 23.140 | |
| plot_rank_bias | 0.000 | 0.000 | 0.001 | |
| pos_neg_marker | 0.012 | 0.000 | 0.013 | |
| pos_neg_select | 0.144 | 0.000 | 0.232 | |
| query_rank_bias | 0.080 | 0.000 | 0.092 | |
| ref_feature_select | 0.072 | 0.000 | 0.072 | |
| ref_marker_select | 0.264 | 0.000 | 0.268 | |
| reverse_marker_matrix | 0.005 | 0.000 | 0.005 | |
| run_clustifyr_app | 0 | 0 | 0 | |
| seurat_meta | 0 | 0 | 0 | |
| seurat_ref | 0.000 | 0.003 | 0.002 | |
| write_meta | 0.108 | 0.001 | 0.110 | |