Multiple platform build/check report for BioC 3.12 - CHECK report for clustifyr on tokay1

Package: clustifyr

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clustifyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings clustifyr_1.2.0.tar.gz

StartedAt: 2021-05-06 01:33:33 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 01:44:52 -0400 (Thu, 06 May 2021)

EllapsedTime: 679.0 seconds

RetCode: 0

Status: OK

CheckDir: clustifyr.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clustifyr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings clustifyr_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/clustifyr.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.2.0'
* 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
plot_pathway_gsea 5.45   0.03    5.49
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plot_pathway_gsea 6.26      0    6.27
* 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://172.29.0.3/BBS/3.12/bioc/src/contrib/clustifyr_1.2.0.tar.gz && rm -rf clustifyr.buildbin-libdir && mkdir clustifyr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clustifyr.buildbin-libdir clustifyr_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL clustifyr_1.2.0.zip && rm clustifyr_1.2.0.tar.gz clustifyr_1.2.0.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 2333k  100 2333k    0     0  26.8M      0 --:--:-- --:--:-- --:--:-- 27.1M

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  
    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  
    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  
    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_1.2.0.zip
* DONE (clustifyr)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'clustifyr' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 172 ]
> 
> proc.time()
   user  system elapsed 
 135.85    5.40  148.31


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 172 ]
> 
> proc.time()
   user  system elapsed 
 188.57    4.56  193.50

name	user	system	elapsed
append_genes	0.05	0.00	0.04
average_clusters	0.17	0.00	0.17
binarize_expr	0.08	0.01	0.09
calculate_pathway_gsea	4.57	0.03	4.61
call_consensus	0.22	0.04	0.25
call_to_metadata	0	0	0
check_raw_counts	1.44	0.04	1.49
clustify	0.25	0.05	0.29
clustify_lists	0.20	0.04	0.25
clustify_nudge	1.02	0.33	1.34
collapse_to_cluster	1.03	0.16	1.19
compare_lists	0.22	0.01	0.24
cor_to_call	0.11	0.00	0.10
cor_to_call_rank	0.12	0.00	0.13
cor_to_call_topn	0.13	0.00	0.12
downsample_matrix	0.12	0.00	0.13
feature_select_PCA	0.05	0.00	0.04
file_marker_parse	0	0	0
find_rank_bias	0.15	0.05	0.21
gene_pct_markerm	0.60	0.00	0.59
get_ucsc_reference	0	0	0
get_vargenes	0	0	0
gmt_to_list	0.25	0.04	0.29
insert_meta_object	0	0	0
marker_select	0.04	0.00	0.04
matrixize_markers	0.05	0.00	0.05
object_data	0.06	0.00	0.06
object_ref	0	0	0
overcluster	1.92	0.14	2.06
overcluster_test	1.70	0.01	1.72
parse_loc_object	0	0	0
plot_best_call	0.71	0.02	0.72
plot_cor	0.79	0.09	0.89
plot_cor_heatmap	1.27	0.03	1.30
plot_dims	0.48	0.08	0.56
plot_gene	0.71	0.00	0.70
plot_pathway_gsea	5.45	0.03	5.49
pos_neg_marker	0.02	0.00	0.01
pos_neg_select	0.06	0.00	0.06
ref_feature_select	0.08	0.00	0.08
ref_marker_select	0.34	0.00	0.35
reverse_marker_matrix	0.02	0.00	0.01
run_gsea	0.53	0.00	0.53
seurat_meta	0	0	0
seurat_ref	0.01	0.00	0.02
write_meta	0.17	0.00	0.17

name	user	system	elapsed
append_genes	0.03	0.00	0.03
average_clusters	0.08	0.03	0.11
binarize_expr	0.78	0.00	0.78
calculate_pathway_gsea	3.84	0.05	3.89
call_consensus	0.31	0.00	0.32
call_to_metadata	0	0	0
check_raw_counts	1.30	0.12	1.42
clustify	0.28	0.05	0.33
clustify_lists	0.28	0.03	0.31
clustify_nudge	1.08	0.05	1.12
collapse_to_cluster	1.53	0.07	1.61
compare_lists	0.24	0.00	0.24
cor_to_call	0.12	0.00	0.12
cor_to_call_rank	0.10	0.04	0.13
cor_to_call_topn	0.15	0.00	0.15
downsample_matrix	0.14	0.04	0.19
feature_select_PCA	0.02	0.00	0.02
file_marker_parse	0.01	0.00	0.01
find_rank_bias	0.25	0.02	0.27
gene_pct_markerm	0.58	0.00	0.58
get_ucsc_reference	0	0	0
get_vargenes	0	0	0
gmt_to_list	0.16	0.00	0.15
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	0.01	0.00	0.02
overcluster	2.07	0.14	2.20
overcluster_test	1.56	0.05	1.61
parse_loc_object	0	0	0
plot_best_call	0.87	0.00	0.87
plot_cor	0.68	0.03	0.71
plot_cor_heatmap	1.21	0.03	1.25
plot_dims	0.38	0.00	0.37
plot_gene	0.61	0.00	0.61
plot_pathway_gsea	6.26	0.00	6.27
pos_neg_marker	0.02	0.00	0.01
pos_neg_select	0.14	0.00	0.14
ref_feature_select	0.06	0.00	0.07
ref_marker_select	0.24	0.00	0.23
reverse_marker_matrix	0	0	0
run_gsea	1.23	0.00	1.24
seurat_meta	0	0	0
seurat_ref	0.02	0.00	0.01
write_meta	0.11	0.00	0.11

CHECK report for clustifyr on tokay1

Summary

Command output

Installation output

Tests output

Example timings