| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-31 05:44:31 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 365/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| clustifyr 1.13.0 (landing page) Kent Riemondy
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: clustifyr |
| Version: 1.13.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings clustifyr_1.13.0.tar.gz |
| StartedAt: 2023-05-30 03:43:50 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 03:59:09 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 919.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: clustifyr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings clustifyr_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/clustifyr.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘clustifyr/DESCRIPTION’ ... OK
* this is package ‘clustifyr’ version ‘1.13.0’
* 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 20.070 0.284 20.355
calculate_pathway_gsea 17.294 0.588 17.883
* 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/R/R-4.3.0/bin/R CMD INSTALL clustifyr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
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
580.583 5.009 585.584
clustifyr.Rcheck/clustifyr-Ex.timings
| name | user | system | elapsed | |
| append_genes | 0.032 | 0.008 | 0.040 | |
| assess_rank_bias | 0 | 0 | 0 | |
| average_clusters | 0.117 | 0.020 | 0.137 | |
| binarize_expr | 0.071 | 0.004 | 0.075 | |
| build_atlas | 0.857 | 0.048 | 0.906 | |
| calc_distance | 0.002 | 0.003 | 0.005 | |
| calculate_pathway_gsea | 17.294 | 0.588 | 17.883 | |
| call_consensus | 0.343 | 0.012 | 0.356 | |
| call_to_metadata | 0.179 | 0.096 | 0.276 | |
| check_raw_counts | 0.927 | 0.080 | 1.007 | |
| clustify | 0.262 | 0.004 | 0.266 | |
| clustify_lists | 0.117 | 0.008 | 0.125 | |
| clustify_nudge | 1.097 | 0.028 | 1.125 | |
| clustifyr_methods | 0.000 | 0.000 | 0.001 | |
| collapse_to_cluster | 2.903 | 0.072 | 2.975 | |
| compare_lists | 0.923 | 0.052 | 0.975 | |
| cor_to_call | 0.111 | 0.000 | 0.111 | |
| cor_to_call_rank | 0.118 | 0.004 | 0.122 | |
| cor_to_call_topn | 0.127 | 0.000 | 0.128 | |
| downsample_matrix | 0.119 | 0.000 | 0.119 | |
| feature_select_PCA | 0.010 | 0.003 | 0.013 | |
| file_marker_parse | 0.002 | 0.000 | 0.003 | |
| find_rank_bias | 0.066 | 0.000 | 0.066 | |
| gene_pct_markerm | 0.772 | 0.012 | 0.784 | |
| get_ucsc_reference | 0 | 0 | 0 | |
| get_vargenes | 0.001 | 0.000 | 0.001 | |
| gmt_to_list | 0.414 | 0.064 | 0.476 | |
| insert_meta_object | 0 | 0 | 0 | |
| make_comb_ref | 0.034 | 0.008 | 0.042 | |
| marker_select | 0.056 | 0.004 | 0.060 | |
| matrixize_markers | 0.038 | 0.008 | 0.045 | |
| object_data | 0.057 | 0.004 | 0.062 | |
| object_ref | 0.002 | 0.004 | 0.006 | |
| overcluster | 3.191 | 0.064 | 3.255 | |
| overcluster_test | 1.735 | 0.040 | 1.775 | |
| parse_loc_object | 0.000 | 0.000 | 0.001 | |
| plot_best_call | 0.746 | 0.028 | 0.774 | |
| plot_cor | 0.738 | 0.004 | 0.741 | |
| plot_cor_heatmap | 1.206 | 0.016 | 1.222 | |
| plot_dims | 0.447 | 0.008 | 0.455 | |
| plot_gene | 0.646 | 0.004 | 0.650 | |
| plot_pathway_gsea | 20.070 | 0.284 | 20.355 | |
| plot_rank_bias | 0.000 | 0.000 | 0.001 | |
| pos_neg_marker | 0.007 | 0.004 | 0.012 | |
| pos_neg_select | 0.146 | 0.004 | 0.151 | |
| query_rank_bias | 0.076 | 0.000 | 0.077 | |
| ref_feature_select | 0.060 | 0.008 | 0.068 | |
| ref_marker_select | 0.277 | 0.008 | 0.286 | |
| reverse_marker_matrix | 0.002 | 0.004 | 0.006 | |
| run_clustifyr_app | 0.000 | 0.000 | 0.001 | |
| seurat_meta | 0.000 | 0.000 | 0.001 | |
| seurat_ref | 0.003 | 0.000 | 0.003 | |
| write_meta | 0.113 | 0.000 | 0.112 | |