Multiple platform build/check report for BioC 3.13 - CHECK results for clustifyr on tokay2

Package: clustifyr

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clustifyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings clustifyr_1.4.0.tar.gz

StartedAt: 2021-10-14 21:16:10 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 21:24:57 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 526.2 seconds

RetCode: 0

Status: OK

CheckDir: clustifyr.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clustifyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings clustifyr_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/clustifyr.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.4.0'
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 http://155.52.207.165/BBS/3.13/bioc/src/contrib/clustifyr_1.4.0.tar.gz && rm -rf clustifyr.buildbin-libdir && mkdir clustifyr.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clustifyr.buildbin-libdir clustifyr_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL clustifyr_1.4.0.zip && rm clustifyr_1.4.0.tar.gz clustifyr_1.4.0.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
 46 2811k   46 1299k    0     0  1474k      0  0:00:01 --:--:--  0:00:01 1475k
100 2811k  100 2811k    0     0  1785k      0  0:00:01  0:00:01 --:--:-- 1786k

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
    append_genes                            html  
    assess_rank_bias                        html  
    assign_ident                            html  
    average_clusters                        html  
    binarize_expr                           html  
    build_atlas                             html  
    calc_similarity                         html  
    calculate_pathway_gsea                  html  
    call_consensus                          html  
    call_to_metadata                        html  
    cbmc_m                                  html  
    cbmc_ref                                html  
    check_raw_counts                        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_ucsc_reference                      html  
    get_unique_column                       html  
    get_vargenes                            html  
    gmt_to_list                             html  
    human_genes_10x                         html  
    insert_meta_object                      html  
    install_clustifyr_app                   html  
    kl_divergence                           html  
    make_comb_ref                           html  
    marker_select                           html  
    matrixize_markers                       html  
    mouse_genes_10x                         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  
    plot_rank_bias                          html  
    pos_neg_marker                          html  
    pos_neg_select                          html  
    pretty_palette                          html  
    pretty_palette2                         html  
    pretty_palette_ramp_d                   html  
    query_rank_bias                         html  
    ref_feature_select                      html  
    ref_marker_select                       html  
    reverse_marker_matrix                   html  
    run_clustifyr_app                       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_1.4.0.zip
* DONE (clustifyr)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'clustifyr' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 162 ]
> 
> proc.time()
   user  system elapsed 
 118.60    4.85  123.76


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 162 ]
> 
> proc.time()
   user  system elapsed 
 117.40    3.43  120.86

name	user	system	elapsed
append_genes	0.05	0.01	0.06
assess_rank_bias	0	0	0
average_clusters	0.20	0.02	0.22
binarize_expr	0.55	0.00	0.55
build_atlas	0.09	0.02	0.10
calculate_pathway_gsea	2.41	0.00	2.41
call_consensus	0.18	0.03	0.22
call_to_metadata	0.69	0.03	0.72
check_raw_counts	0.66	0.08	0.73
clustify	0.20	0.03	0.24
clustify_lists	0.17	0.03	0.20
clustify_nudge	0.60	0.09	0.69
clustifyr_methods	0	0	0
collapse_to_cluster	0.76	0.07	0.83
compare_lists	0.17	0.00	0.17
cor_to_call	0.07	0.03	0.09
cor_to_call_rank	0.07	0.01	0.10
cor_to_call_topn	0.08	0.03	0.10
downsample_matrix	0.11	0.03	0.14
feature_select_PCA	0.02	0.02	0.03
file_marker_parse	0	0	0
find_rank_bias	0.06	0.00	0.06
gene_pct_markerm	0.34	0.00	0.35
get_ucsc_reference	0	0	0
get_vargenes	0	0	0
gmt_to_list	0.39	0.02	0.44
insert_meta_object	0	0	0
install_clustifyr_app	0	0	0
make_comb_ref	0.02	0.00	0.02
marker_select	0.03	0.00	0.03
matrixize_markers	0.03	0.01	0.05
object_data	0.03	0.03	0.06
object_ref	0	0	0
overcluster	1.28	0.07	1.35
overcluster_test	1.03	0.04	1.08
parse_loc_object	0	0	0
plot_best_call	0.55	0.03	0.57
plot_cor	0.51	0.11	0.63
plot_cor_heatmap	0.80	0.04	0.83
plot_dims	0.28	0.01	0.29
plot_gene	0.42	0.00	0.43
plot_pathway_gsea	3.27	0.05	3.31
plot_rank_bias	0	0	0
pos_neg_marker	0.01	0.00	0.01
pos_neg_select	0.05	0.01	0.07
query_rank_bias	0.05	0.02	0.06
ref_feature_select	0.05	0.01	0.06
ref_marker_select	0.17	0.02	0.18
reverse_marker_matrix	0	0	0
run_clustifyr_app	0	0	0
run_gsea	0.32	0.03	0.35
seurat_meta	0	0	0
seurat_ref	0	0	0
write_meta	0.28	0.00	0.28

name	user	system	elapsed
append_genes	0.57	0.00	0.58
assess_rank_bias	0	0	0
average_clusters	0.05	0.05	0.09
binarize_expr	0.08	0.00	0.08
build_atlas	0.11	0.00	0.11
calculate_pathway_gsea	2.76	0.01	2.78
call_consensus	0.30	0.02	0.31
call_to_metadata	0.27	0.05	0.31
check_raw_counts	1.33	0.01	1.35
clustify	0.21	0.00	0.22
clustify_lists	0.21	0.02	0.21
clustify_nudge	0.58	0.00	0.58
clustifyr_methods	0	0	0
collapse_to_cluster	1.20	0.03	1.24
compare_lists	0.15	0.00	0.15
cor_to_call	0.08	0.02	0.10
cor_to_call_rank	0.05	0.01	0.07
cor_to_call_topn	0.09	0.00	0.09
downsample_matrix	0.09	0.00	0.09
feature_select_PCA	0.02	0.00	0.02
file_marker_parse	0	0	0
find_rank_bias	0.05	0.00	0.05
gene_pct_markerm	0.32	0.00	0.32
get_ucsc_reference	0	0	0
get_vargenes	0	0	0
gmt_to_list	0.37	0.00	0.37
insert_meta_object	0	0	0
install_clustifyr_app	0	0	0
make_comb_ref	0.02	0.00	0.02
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	1.59	0.11	1.70
overcluster_test	1.39	0.06	1.46
parse_loc_object	0	0	0
plot_best_call	0.60	0.03	0.62
plot_cor	0.53	0.02	0.55
plot_cor_heatmap	0.78	0.06	0.84
plot_dims	0.3	0.0	0.3
plot_gene	0.48	0.00	0.48
plot_pathway_gsea	3.83	0.00	3.83
plot_rank_bias	0	0	0
pos_neg_marker	0.01	0.00	0.02
pos_neg_select	0.07	0.02	0.07
query_rank_bias	0.04	0.00	0.05
ref_feature_select	0.07	0.00	0.06
ref_marker_select	0.23	0.00	0.24
reverse_marker_matrix	0	0	0
run_clustifyr_app	0	0	0
run_gsea	1.38	0.01	1.39
seurat_meta	0	0	0
seurat_ref	0.01	0.00	0.01
write_meta	0.39	0.00	0.39

CHECK results for clustifyr on tokay2

Summary

Command output

Installation output

Tests output

Example timings