Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:07 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for clustifyr on tokay2


To the developers/maintainers of the clustifyr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clustifyr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 344/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.6.0  (landing page)
Rui Fu
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/clustifyr
git_branch: RELEASE_3_14
git_last_commit: e07d1df
git_last_commit_date: 2021-10-26 12:57:20 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.6.0
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: 2022-01-20 17:43:43 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 17:52:53 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 549.2 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

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


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/clustifyr.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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.



Installation output

clustifyr.Rcheck/00install.out

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


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  5 2811k    5  164k    0     0   736k      0  0:00:03 --:--:--  0:00:03  735k
100 2811k  100 2811k    0     0  2851k      0 --:--:-- --:--:-- --:--:-- 2851k

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

Tests output

clustifyr.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 167 ]
> 
> proc.time()
   user  system elapsed 
 125.73    5.90  132.32 

clustifyr.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 167 ]
> 
> proc.time()
   user  system elapsed 
 127.09    3.93  131.00 

Example timings

clustifyr.Rcheck/examples_i386/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.070.010.08
assess_rank_bias000
average_clusters0.300.020.31
binarize_expr0.770.010.78
build_atlas0.070.050.12
calculate_pathway_gsea2.530.002.54
call_consensus0.220.010.23
call_to_metadata0.220.070.30
check_raw_counts1.210.091.29
clustify0.190.050.23
clustify_lists0.090.000.10
clustify_nudge0.710.060.76
clustifyr_methods000
collapse_to_cluster1.290.131.43
compare_lists0.160.010.17
cor_to_call0.080.000.08
cor_to_call_rank0.070.000.07
cor_to_call_topn0.10.00.1
downsample_matrix0.140.020.15
feature_select_PCA0.010.000.02
file_marker_parse000
find_rank_bias0.070.030.09
gene_pct_markerm0.430.140.58
get_ucsc_reference000
get_vargenes000
gmt_to_list0.340.230.57
insert_meta_object000
make_comb_ref0.020.000.02
marker_select0.050.000.05
matrixize_markers0.010.020.03
object_data0.050.000.05
object_ref000
overcluster0.890.111.00
overcluster_test1.170.011.18
parse_loc_object000
plot_best_call0.590.000.59
plot_cor0.560.000.56
plot_cor_heatmap0.910.050.96
plot_dims0.250.000.25
plot_gene0.50.00.5
plot_pathway_gsea3.300.003.29
plot_rank_bias000
pos_neg_marker0.010.000.02
pos_neg_select0.060.000.06
query_rank_bias0.040.020.05
ref_feature_select0.060.000.06
ref_marker_select0.200.000.21
reverse_marker_matrix000
run_clustifyr_app000
run_gsea0.240.000.23
seurat_meta000
seurat_ref000
write_meta0.290.000.30

clustifyr.Rcheck/examples_x64/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.570.000.56
assess_rank_bias000
average_clusters0.070.000.08
binarize_expr0.080.000.07
build_atlas0.110.000.11
calculate_pathway_gsea2.610.012.62
call_consensus0.170.000.18
call_to_metadata0.160.050.20
check_raw_counts1.20.01.2
clustify0.210.000.21
clustify_lists0.070.020.09
clustify_nudge0.550.000.55
clustifyr_methods000
collapse_to_cluster1.340.041.37
compare_lists0.160.000.16
cor_to_call0.050.030.08
cor_to_call_rank0.080.020.09
cor_to_call_topn0.060.030.09
downsample_matrix0.090.020.11
feature_select_PCA0.020.000.02
file_marker_parse000
find_rank_bias0.060.010.08
gene_pct_markerm0.340.000.34
get_ucsc_reference000
get_vargenes000
gmt_to_list0.300.030.33
insert_meta_object000
make_comb_ref000
marker_select0.020.020.03
matrixize_markers0.010.000.02
object_data0.070.000.06
object_ref000
overcluster1.420.121.55
overcluster_test1.110.021.12
parse_loc_object000
plot_best_call0.580.030.61
plot_cor0.570.000.57
plot_cor_heatmap0.970.010.99
plot_dims0.250.000.25
plot_gene0.610.000.61
plot_pathway_gsea3.860.003.86
plot_rank_bias000
pos_neg_marker0.020.000.01
pos_neg_select0.060.000.07
query_rank_bias0.050.000.05
ref_feature_select0.060.000.06
ref_marker_select0.20.00.2
reverse_marker_matrix0.020.000.02
run_clustifyr_app000
run_gsea0.230.010.25
seurat_meta000
seurat_ref000
write_meta0.310.000.31