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This page was generated on 2021-09-24 15:06:05 -0400 (Fri, 24 Sep 2021).

CHECK results for clustifyr on tokay2

To the developers/maintainers of the clustifyr package:
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raw results

Package 336/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.4.0  (landing page)
Rui Fu
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/clustifyr
git_branch: RELEASE_3_13
git_last_commit: 7a53859
git_last_commit_date: 2021-05-19 12:49:30 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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: 2021-09-23 20:34:24 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 20:43:12 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 528.3 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* 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


Installation output

clustifyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 42 2811k   42 1198k    0     0  1959k      0  0:00:01 --:--:--  0:00:01 1961k
100 2811k  100 2811k    0     0  2558k      0  0:00:01  0:00:01 --:--:-- 2560k

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

Tests output

clustifyr.Rcheck/tests_i386/testthat.Rout


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 
 117.06    4.90  123.48 

clustifyr.Rcheck/tests_x64/testthat.Rout


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 
 120.82    4.03  124.87 

Example timings

clustifyr.Rcheck/examples_i386/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.080.000.07
assess_rank_bias000
average_clusters0.250.000.25
binarize_expr0.530.000.53
build_atlas0.110.020.13
calculate_pathway_gsea2.760.002.76
call_consensus0.190.020.21
call_to_metadata0.660.030.68
check_raw_counts0.650.080.74
clustify0.190.040.23
clustify_lists0.140.060.20
clustify_nudge0.630.110.74
clustifyr_methods000
collapse_to_cluster0.780.040.81
compare_lists0.150.000.16
cor_to_call0.070.010.08
cor_to_call_rank0.070.000.07
cor_to_call_topn0.080.020.10
downsample_matrix0.110.010.12
feature_select_PCA0.030.000.03
file_marker_parse000
find_rank_bias0.050.000.05
gene_pct_markerm0.340.000.34
get_ucsc_reference000
get_vargenes000
gmt_to_list0.490.000.49
insert_meta_object000
install_clustifyr_app000
make_comb_ref0.030.000.03
marker_select0.030.020.05
matrixize_markers0.020.030.04
object_data0.070.030.11
object_ref000
overcluster1.490.161.64
overcluster_test1.250.041.30
parse_loc_object000
plot_best_call0.550.030.58
plot_cor0.560.130.69
plot_cor_heatmap0.810.080.89
plot_dims0.310.030.34
plot_gene0.460.000.45
plot_pathway_gsea3.680.003.69
plot_rank_bias000
pos_neg_marker0.020.000.02
pos_neg_select0.050.010.06
query_rank_bias0.040.000.04
ref_feature_select0.10.00.1
ref_marker_select0.20.00.2
reverse_marker_matrix0.020.000.01
run_clustifyr_app000
run_gsea0.390.000.40
seurat_meta000
seurat_ref000
write_meta0.310.020.32

clustifyr.Rcheck/examples_x64/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.570.000.58
assess_rank_bias000
average_clusters0.070.020.08
binarize_expr0.070.000.07
build_atlas0.10.00.1
calculate_pathway_gsea2.720.002.72
call_consensus0.170.000.17
call_to_metadata0.190.010.20
check_raw_counts1.200.081.28
clustify0.160.050.21
clustify_lists0.170.000.17
clustify_nudge0.620.010.64
clustifyr_methods000
collapse_to_cluster1.360.051.41
compare_lists0.170.000.17
cor_to_call0.090.000.10
cor_to_call_rank0.080.000.07
cor_to_call_topn0.080.000.08
downsample_matrix0.080.010.10
feature_select_PCA000
file_marker_parse000
find_rank_bias0.070.000.06
gene_pct_markerm0.320.000.33
get_ucsc_reference000
get_vargenes000
gmt_to_list0.360.020.38
insert_meta_object000
install_clustifyr_app000
make_comb_ref0.020.000.01
marker_select0.030.000.03
matrixize_markers0.030.000.04
object_data0.050.000.04
object_ref0.010.000.02
overcluster1.460.141.59
overcluster_test1.200.031.24
parse_loc_object000
plot_best_call0.730.030.77
plot_cor0.660.020.67
plot_cor_heatmap0.860.050.91
plot_dims0.280.010.29
plot_gene0.480.030.52
plot_pathway_gsea4.380.024.39
plot_rank_bias000
pos_neg_marker000
pos_neg_select0.060.010.08
query_rank_bias0.050.000.05
ref_feature_select0.080.000.08
ref_marker_select0.220.000.22
reverse_marker_matrix000
run_clustifyr_app000
run_gsea1.000.031.03
seurat_meta000
seurat_ref000
write_meta0.310.000.31