Kent Riemondy
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| 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 2023-11-02 11:40:32 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: clustifyr |
| Version: 1.14.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings clustifyr_1.14.0.tar.gz |
| StartedAt: 2023-11-02 09:22:15 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 09:30:23 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 487.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: clustifyr.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings clustifyr_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/clustifyr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 20.153 2.921 25.990
calculate_pathway_gsea 17.683 1.008 18.852
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 810298 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
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* 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: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/clustifyr.Rcheck/00check.log’
for details.
clustifyr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL clustifyr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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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clustifyr.Rcheck/clustifyr-Ex.timings
| name | user | system | elapsed | |
| append_genes | 0.049 | 0.015 | 0.072 | |
| assess_rank_bias | 0 | 0 | 0 | |
| average_clusters | 0.913 | 0.041 | 0.957 | |
| binarize_expr | 0.059 | 0.008 | 0.067 | |
| build_atlas | 0.102 | 0.012 | 0.114 | |
| calc_distance | 0.004 | 0.000 | 0.004 | |
| calculate_pathway_gsea | 17.683 | 1.008 | 18.852 | |
| call_consensus | 0.316 | 0.017 | 0.336 | |
| call_to_metadata | 0.150 | 0.076 | 0.226 | |
| check_raw_counts | 0.917 | 0.032 | 0.951 | |
| clustify | 0.252 | 0.003 | 0.267 | |
| clustify_lists | 0.097 | 0.012 | 0.111 | |
| clustify_nudge | 0.797 | 0.008 | 0.808 | |
| clustifyr_methods | 0.001 | 0.000 | 0.000 | |
| collapse_to_cluster | 2.933 | 0.143 | 3.204 | |
| compare_lists | 0.950 | 0.028 | 0.981 | |
| cor_to_call | 0.1 | 0.0 | 0.1 | |
| cor_to_call_rank | 0.100 | 0.004 | 0.104 | |
| cor_to_call_topn | 0.112 | 0.000 | 0.112 | |
| downsample_matrix | 0.048 | 0.003 | 0.052 | |
| feature_select_PCA | 0.014 | 0.001 | 0.021 | |
| file_marker_parse | 0.002 | 0.000 | 0.007 | |
| find_rank_bias | 0.049 | 0.004 | 0.055 | |
| gene_pct_markerm | 0.507 | 0.027 | 0.546 | |
| get_ucsc_reference | 0.001 | 0.000 | 0.000 | |
| get_vargenes | 0 | 0 | 0 | |
| gmt_to_list | 0.051 | 0.000 | 0.063 | |
| insert_meta_object | 0.000 | 0.000 | 0.001 | |
| make_comb_ref | 0.037 | 0.003 | 0.042 | |
| marker_select | 0.032 | 0.000 | 0.034 | |
| matrixize_markers | 0.034 | 0.008 | 0.043 | |
| object_data | 0.049 | 0.004 | 0.053 | |
| object_ref | 0.001 | 0.004 | 0.005 | |
| overcluster | 3.064 | 0.047 | 3.130 | |
| overcluster_test | 1.637 | 0.037 | 1.698 | |
| parse_loc_object | 0.000 | 0.000 | 0.001 | |
| plot_best_call | 0.671 | 0.020 | 0.692 | |
| plot_cor | 0.647 | 0.004 | 0.651 | |
| plot_cor_heatmap | 1.159 | 0.011 | 1.205 | |
| plot_dims | 0.445 | 0.000 | 0.446 | |
| plot_gene | 0.599 | 0.003 | 0.604 | |
| plot_pathway_gsea | 20.153 | 2.921 | 25.990 | |
| plot_rank_bias | 0.000 | 0.000 | 0.001 | |
| pos_neg_marker | 0.011 | 0.000 | 0.011 | |
| pos_neg_select | 0.125 | 0.007 | 0.137 | |
| query_rank_bias | 0.069 | 0.001 | 0.071 | |
| ref_feature_select | 0.054 | 0.004 | 0.059 | |
| ref_marker_select | 0.273 | 0.000 | 0.274 | |
| reverse_marker_matrix | 0.002 | 0.003 | 0.005 | |
| run_clustifyr_app | 0 | 0 | 0 | |
| seurat_meta | 0.001 | 0.000 | 0.001 | |
| seurat_ref | 0.003 | 0.000 | 0.003 | |
| write_meta | 0.116 | 0.000 | 0.119 | |