Multiple platform build/check report for BioC 3.14 - CHECK results for clustifyr on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: clustifyr

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clustifyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings clustifyr_1.6.0.tar.gz

StartedAt: 2022-04-12 17:31:10 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 17:40:31 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 561.9 seconds

RetCode: 0

Status: OK

CheckDir: clustifyr.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clustifyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings clustifyr_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/clustifyr.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.6.0'
* 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 ... NOTE
assess_rank_bias : <anonymous>: no visible binding for '<<-' assignment
  to 'res3'
assess_rank_bias: no visible binding for global variable 'res3'
average_clusters : <anonymous>: no visible binding for global variable
  'pbmc_matrix_small'
Undefined global functions or variables:
  pbmc_matrix_small res3
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/clustifyr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/clustifyr_1.6.0.tar.gz && rm -rf clustifyr.buildbin-libdir && mkdir clustifyr.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clustifyr.buildbin-libdir clustifyr_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL clustifyr_1.6.0.zip && rm clustifyr_1.6.0.tar.gz clustifyr_1.6.0.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
 22 2811k   22  641k    0     0  1698k      0  0:00:01 --:--:--  0:00:01 1698k
100 2811k  100 2811k    0     0  2605k      0  0:00:01  0:00:01 --:--:-- 2608k

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  
    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_1.6.0.zip
* DONE (clustifyr)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'clustifyr' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 167 ]
> 
> proc.time()
   user  system elapsed 
 120.90    6.07  127.07


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 167 ]
> 
> proc.time()
   user  system elapsed 
 136.01    3.60  139.60

name	user	system	elapsed
append_genes	0.16	0.02	0.17
assess_rank_bias	0	0	0
average_clusters	0.58	0.06	0.64
binarize_expr	0.07	0.02	0.08
build_atlas	0.07	0.03	0.11
calculate_pathway_gsea	2.41	0.06	2.47
call_consensus	0.31	0.00	0.31
call_to_metadata	0.22	0.03	0.25
check_raw_counts	1.24	0.06	1.30
clustify	0.23	0.07	0.30
clustify_lists	0.08	0.01	0.09
clustify_nudge	0.65	0.07	0.72
clustifyr_methods	0	0	0
collapse_to_cluster	0.79	0.10	0.89
compare_lists	0.17	0.02	0.19
cor_to_call	0.09	0.00	0.09
cor_to_call_rank	0.09	0.00	0.09
cor_to_call_topn	0.11	0.00	0.11
downsample_matrix	0.11	0.03	0.14
feature_select_PCA	0.03	0.00	0.04
file_marker_parse	0.00	0.02	0.01
find_rank_bias	0.07	0.00	0.06
gene_pct_markerm	0.37	0.00	0.38
get_ucsc_reference	0	0	0
get_vargenes	0	0	0
gmt_to_list	0.35	0.04	0.39
insert_meta_object	0	0	0
make_comb_ref	0.01	0.00	0.01
marker_select	0.05	0.00	0.05
matrixize_markers	0.05	0.00	0.05
object_data	0.06	0.02	0.08
object_ref	0.01	0.00	0.01
overcluster	1.24	0.12	1.36
overcluster_test	1.03	0.15	1.17
parse_loc_object	0	0	0
plot_best_call	0.58	0.01	0.60
plot_cor	0.53	0.02	0.54
plot_cor_heatmap	0.84	0.09	0.94
plot_dims	0.30	0.06	0.36
plot_gene	0.47	0.00	0.47
plot_pathway_gsea	3.47	0.02	3.48
plot_rank_bias	0	0	0
pos_neg_marker	0.02	0.00	0.02
pos_neg_select	0.06	0.00	0.06
query_rank_bias	0.03	0.02	0.05
ref_feature_select	0.06	0.02	0.08
ref_marker_select	0.19	0.01	0.20
reverse_marker_matrix	0.02	0.00	0.02
run_clustifyr_app	0	0	0
run_gsea	0.34	0.02	0.36
seurat_meta	0	0	0
seurat_ref	0	0	0
write_meta	0.33	0.01	0.34

name	user	system	elapsed
append_genes	0.05	0.00	0.05
assess_rank_bias	0	0	0
average_clusters	0.71	0.00	0.72
binarize_expr	0.05	0.03	0.07
build_atlas	0.11	0.00	0.11
calculate_pathway_gsea	2.95	0.03	2.98
call_consensus	0.33	0.02	0.35
call_to_metadata	0.15	0.06	0.22
check_raw_counts	1.66	0.03	1.68
clustify	0.25	0.00	0.25
clustify_lists	0.08	0.05	0.13
clustify_nudge	0.67	0.00	0.67
clustifyr_methods	0	0	0
collapse_to_cluster	1.34	0.02	1.36
compare_lists	0.21	0.01	0.22
cor_to_call	0.09	0.00	0.09
cor_to_call_rank	0.09	0.00	0.10
cor_to_call_topn	0.11	0.00	0.11
downsample_matrix	0.14	0.00	0.14
feature_select_PCA	0.02	0.00	0.01
file_marker_parse	0	0	0
find_rank_bias	0.11	0.00	0.11
gene_pct_markerm	0.39	0.00	0.39
get_ucsc_reference	0	0	0
get_vargenes	0	0	0
gmt_to_list	0.45	0.00	0.45
insert_meta_object	0	0	0
make_comb_ref	0.03	0.00	0.03
marker_select	0.02	0.03	0.05
matrixize_markers	0.06	0.00	0.06
object_data	0.08	0.00	0.08
object_ref	0	0	0
overcluster	1.73	0.07	1.80
overcluster_test	1.16	0.01	1.17
parse_loc_object	0.01	0.00	0.01
plot_best_call	0.57	0.03	0.60
plot_cor	0.51	0.05	0.56
plot_cor_heatmap	0.80	0.03	0.83
plot_dims	0.31	0.00	0.31
plot_gene	0.5	0.0	0.5
plot_pathway_gsea	3.59	0.00	3.59
plot_rank_bias	0	0	0
pos_neg_marker	0	0	0
pos_neg_select	0.08	0.00	0.08
query_rank_bias	0.05	0.00	0.05
ref_feature_select	0.06	0.00	0.07
ref_marker_select	0.22	0.00	0.22
reverse_marker_matrix	0	0	0
run_clustifyr_app	0	0	0
run_gsea	0.27	0.00	0.26
seurat_meta	0	0	0
seurat_ref	0	0	0
write_meta	0.34	0.00	0.35

CHECK results for clustifyr on tokay2

Summary

Command output

Installation output

Tests output

Example timings