| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:23 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 349/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| clustifyr 1.11.1 (landing page) Kent Riemondy
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: clustifyr |
| Version: 1.11.1 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clustifyr.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings clustifyr_1.11.1.tar.gz |
| StartedAt: 2022-12-28 22:34:41 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 22:43:34 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 533.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: clustifyr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clustifyr.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings clustifyr_1.11.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/clustifyr.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 12.60 0.06 12.73
calculate_pathway_gsea 10.28 0.00 10.30
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
clustifyr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL clustifyr ### ############################################################################## ############################################################################## * installing to library 'F:/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) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 1 | SKIP 0 | PASS 176 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 176 ]
>
> proc.time()
user system elapsed
337.56 3.09 341.73
clustifyr.Rcheck/clustifyr-Ex.timings
| name | user | system | elapsed | |
| append_genes | 0.04 | 0.00 | 0.05 | |
| assess_rank_bias | 0.00 | 0.02 | 0.01 | |
| average_clusters | 0.6 | 0.0 | 0.6 | |
| binarize_expr | 0.06 | 0.00 | 0.06 | |
| build_atlas | 0.06 | 0.01 | 0.08 | |
| calc_distance | 0.00 | 0.02 | 0.01 | |
| calculate_pathway_gsea | 10.28 | 0.00 | 10.30 | |
| call_consensus | 0.27 | 0.01 | 0.29 | |
| call_to_metadata | 0.30 | 0.13 | 0.42 | |
| check_raw_counts | 0.53 | 0.00 | 0.53 | |
| clustify | 0.19 | 0.00 | 0.19 | |
| clustify_lists | 0.06 | 0.00 | 0.06 | |
| clustify_nudge | 0.45 | 0.00 | 0.45 | |
| clustifyr_methods | 0 | 0 | 0 | |
| collapse_to_cluster | 1.00 | 0.03 | 1.03 | |
| compare_lists | 0.14 | 0.01 | 0.16 | |
| cor_to_call | 0.06 | 0.00 | 0.06 | |
| cor_to_call_rank | 0.11 | 0.02 | 0.13 | |
| cor_to_call_topn | 0.11 | 0.00 | 0.11 | |
| downsample_matrix | 0.13 | 0.00 | 0.12 | |
| feature_select_PCA | 0.00 | 0.02 | 0.01 | |
| file_marker_parse | 0 | 0 | 0 | |
| find_rank_bias | 0.08 | 0.00 | 0.08 | |
| gene_pct_markerm | 0.32 | 0.00 | 0.33 | |
| get_ucsc_reference | 0 | 0 | 0 | |
| get_vargenes | 0 | 0 | 0 | |
| gmt_to_list | 0.32 | 0.03 | 0.36 | |
| insert_meta_object | 0 | 0 | 0 | |
| make_comb_ref | 0.02 | 0.00 | 0.02 | |
| marker_select | 0.01 | 0.00 | 0.01 | |
| matrixize_markers | 0.02 | 0.03 | 0.05 | |
| object_data | 0.05 | 0.00 | 0.05 | |
| object_ref | 0 | 0 | 0 | |
| overcluster | 1.31 | 0.00 | 1.31 | |
| overcluster_test | 1.06 | 0.05 | 1.11 | |
| parse_loc_object | 0 | 0 | 0 | |
| plot_best_call | 0.52 | 0.05 | 0.56 | |
| plot_cor | 0.54 | 0.00 | 0.55 | |
| plot_cor_heatmap | 0.75 | 0.07 | 0.83 | |
| plot_dims | 0.36 | 0.00 | 0.36 | |
| plot_gene | 0.57 | 0.02 | 0.58 | |
| plot_pathway_gsea | 12.60 | 0.06 | 12.73 | |
| plot_rank_bias | 0 | 0 | 0 | |
| pos_neg_marker | 0 | 0 | 0 | |
| pos_neg_select | 0.05 | 0.00 | 0.04 | |
| query_rank_bias | 0.03 | 0.00 | 0.03 | |
| ref_feature_select | 0.07 | 0.00 | 0.07 | |
| ref_marker_select | 0.18 | 0.00 | 0.18 | |
| reverse_marker_matrix | 0 | 0 | 0 | |
| run_clustifyr_app | 0 | 0 | 0 | |
| seurat_meta | 0 | 0 | 0 | |
| seurat_ref | 0 | 0 | 0 | |
| write_meta | 0.06 | 0.00 | 0.06 | |