Multiple platform build/check report for BioC 3.11 - CHECK report for clustifyr on tokay2

Package: clustifyr

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clustifyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings clustifyr_1.0.0.tar.gz

StartedAt: 2020-10-17 02:43:52 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 02:55:00 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 668.1 seconds

RetCode: 0

Status: OK

CheckDir: clustifyr.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clustifyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings clustifyr_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/clustifyr.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clustifyr/DESCRIPTION' ... OK
* this is package 'clustifyr' version '1.0.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
overcluster_test 17.5   0.28    17.8
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
overcluster_test 12.68   0.05   12.73
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/clustifyr_1.0.0.tar.gz && rm -rf clustifyr.buildbin-libdir && mkdir clustifyr.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clustifyr.buildbin-libdir clustifyr_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL clustifyr_1.0.0.zip && rm clustifyr_1.0.0.tar.gz clustifyr_1.0.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2215k  100 2215k    0     0  24.2M      0 --:--:-- --:--:-- --:--:-- 26.3M

install for i386

* 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
  converting help for package 'clustifyr'
    finding HTML links ... done
    assign_ident                            html  
    average_clusters                        html  
    binarize_expr                           html  
    calc_similarity                         html  
    calculate_pathway_gsea                  html  
    call_consensus                          html  
    call_to_metadata                        html  
    cbmc_m                                  html  
    cbmc_ref                                html  
    clustify                                html  
    clustify_lists                          html  
    clustify_nudge                          html  
    clustifyr-package                       html  
    clustifyr_methods                       html  
    collapse_to_cluster                     html  
    compare_lists                           html  
    cor_to_call                             html  
    cor_to_call_rank                        html  
    cor_to_call_topn                        html  
    cosine                                  html  
    downrefs                                html  
    downsample_matrix                       html  
    feature_select_PCA                      html  
    file_marker_parse                       html  
    find_rank_bias                          html  
    gene_pct                                html  
    gene_pct_markerm                        html  
    get_best_match_matrix                   html  
    get_best_str                            html  
    get_common_elements                     html  
    get_similarity                          html  
    get_unique_column                       html  
    get_vargenes                            html  
    gmt_to_list                             html  
    insert_meta_object                      html  
    kl_divergence                           html  
    marker_select                           html  
    matrixize_markers                       html  
    not_pretty_palette                      html  
    object_data                             html  
    object_loc_lookup                       html  
    object_ref                              html  
    overcluster                             html  
    overcluster_test                        html  
    parse_loc_object                        html  
    pbmc_markers                            html  
    pbmc_markers_M3Drop                     html  
    pbmc_matrix_small                       html  
    pbmc_meta                               html  
    pbmc_vargenes                           html  
    percent_clusters                        html  
    permute_similarity                      html  
    plot_best_call                          html  
    plot_call                               html  
    plot_cor                                html  
    plot_cor_heatmap                        html  
    plot_dims                               html  
    plot_gene                               html  
    plot_pathway_gsea                       html  
    pos_neg_marker                          html  
    pos_neg_select                          html  
    pretty_palette                          html  
    pretty_palette2                         html  
    pretty_palette_ramp_d                   html  
    ref_feature_select                      html  
    ref_marker_select                       html  
    reverse_marker_matrix                   html  
    run_gsea                                html  
    s_small                                 html  
    s_small3                                html  
    sce_small                               html  
    seurat_meta                             html  
    seurat_ref                              html  
    vector_similarity                       html  
    write_meta                              html  
*** 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

install for x64

* installing *source* package 'clustifyr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clustifyr' as clustifyr_1.0.0.zip
* DONE (clustifyr)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'clustifyr' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
== testthat results  ===========================================================
[ OK: 159 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 128.85    4.60  164.10


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 159 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 133.51    3.15  152.29

name	user	system	elapsed
average_clusters	0.09	0.04	0.13
binarize_expr	0.13	0.03	0.15
calculate_pathway_gsea	3.70	0.14	3.85
call_consensus	0.28	0.00	0.28
call_to_metadata	0	0	0
clustify	0.86	0.00	0.86
clustify_lists	0.30	0.01	0.31
clustify_nudge	0.97	0.07	1.03
collapse_to_cluster	2.31	0.03	2.34
compare_lists	0.18	0.04	0.22
cor_to_call	0.11	0.00	0.11
cor_to_call_rank	0.10	0.00	0.11
cor_to_call_topn	0.11	0.03	0.14
downsample_matrix	0.21	0.04	0.23
feature_select_PCA	0.01	0.00	0.02
file_marker_parse	0	0	0
find_rank_bias	0.78	0.03	0.81
gene_pct_markerm	0.61	0.00	0.61
get_vargenes	0	0	0
gmt_to_list	0.27	0.01	0.28
insert_meta_object	0	0	0
marker_select	0.05	0.00	0.04
matrixize_markers	0.05	0.00	0.05
object_data	0.08	0.00	0.08
object_ref	0	0	0
overcluster	2.09	0.14	2.23
overcluster_test	17.50	0.28	17.80
parse_loc_object	0	0	0
plot_best_call	0.63	0.00	0.62
plot_cor	0.51	0.00	0.52
plot_cor_heatmap	0.72	0.00	0.72
plot_dims	0.23	0.00	0.23
plot_gene	0.47	0.00	0.47
plot_pathway_gsea	3.07	0.00	3.06
pos_neg_marker	0.01	0.00	0.02
pos_neg_select	0.06	0.00	0.06
ref_feature_select	0.08	0.00	0.08
ref_marker_select	0.17	0.02	0.19
reverse_marker_matrix	0	0	0
run_gsea	0.36	0.00	0.36
seurat_meta	0	0	0
seurat_ref	0	0	0
write_meta	0.11	0.00	0.11

name	user	system	elapsed
average_clusters	0.11	0.05	0.16
binarize_expr	0.11	0.02	0.12
calculate_pathway_gsea	4.93	0.04	4.98
call_consensus	0.26	0.00	0.27
call_to_metadata	0	0	0
clustify	0.33	0.02	0.34
clustify_lists	0.3	0.0	0.3
clustify_nudge	1.37	0.00	1.37
collapse_to_cluster	2.64	0.06	2.71
compare_lists	0.17	0.02	0.19
cor_to_call	0.86	0.01	0.87
cor_to_call_rank	0.11	0.02	0.13
cor_to_call_topn	0.13	0.00	0.12
downsample_matrix	0.21	0.00	0.20
feature_select_PCA	0.01	0.00	0.01
file_marker_parse	0.02	0.00	0.02
find_rank_bias	0.20	0.01	0.22
gene_pct_markerm	0.70	0.02	0.72
get_vargenes	0	0	0
gmt_to_list	0.21	0.03	0.23
insert_meta_object	0	0	0
marker_select	0.03	0.00	0.03
matrixize_markers	0.03	0.00	0.03
object_data	0.05	0.00	0.05
object_ref	0	0	0
overcluster	2.35	0.11	2.45
overcluster_test	12.68	0.05	12.73
parse_loc_object	0	0	0
plot_best_call	0.6	0.0	0.6
plot_cor	0.56	0.00	0.56
plot_cor_heatmap	0.70	0.09	0.80
plot_dims	0.25	0.00	0.25
plot_gene	0.49	0.00	0.48
plot_pathway_gsea	3.5	0.0	3.5
pos_neg_marker	0.01	0.00	0.02
pos_neg_select	0.08	0.00	0.08
ref_feature_select	0.14	0.00	0.14
ref_marker_select	0.31	0.00	0.31
reverse_marker_matrix	0	0	0
run_gsea	0.32	0.02	0.33
seurat_meta	0	0	0
seurat_ref	0	0	0
write_meta	0.11	0.00	0.11

CHECK report for clustifyr on tokay2

Summary

Command output

Installation output

Tests output

Example timings