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

Package: flowGraph

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowGraph.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings flowGraph_1.0.0.tar.gz

StartedAt: 2021-10-14 23:14:13 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 23:20:55 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 401.8 seconds

RetCode: 0

Status: OK

CheckDir: flowGraph.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowGraph.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings flowGraph_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/flowGraph.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 'flowGraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowGraph' version '1.0.0'
* 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 'flowGraph' 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
get_child: no visible binding for global variable 'no_cores'
get_paren: no visible binding for global variable 'no_cores'
ms_psig: no visible binding for global variable 'meta'
Undefined global functions or variables:
  meta no_cores
* 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
fg_save_plots 37.80   0.36   38.37
fg_load       37.39   0.36   37.81
fg_save       36.68   0.46   37.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
fg_save_plots 39.39   0.35   39.73
fg_save       38.93   0.36   39.30
fg_load       36.75   0.44   37.22
* 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-3.13-bioc/meat/flowGraph.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/flowGraph_1.0.0.tar.gz && rm -rf flowGraph.buildbin-libdir && mkdir flowGraph.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowGraph.buildbin-libdir flowGraph_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL flowGraph_1.0.0.zip && rm flowGraph_1.0.0.tar.gz flowGraph_1.0.0.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
100  425k  100  425k    0     0  1131k      0 --:--:-- --:--:-- --:--:-- 1134k

install for i386

* installing *source* package 'flowGraph' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: flowGraph
*** installing help indices
  converting help for package 'flowGraph'
    finding HTML links ... done
    cell_type_layers                        html  
    extract_markers                         html  
    fg_add_feature                          html  
    fg_add_summary                          html  
    fg_clean_phen                           html  
    fg_clear_features                       html  
    fg_clear_summary                        html  
    fg_data_fca                             html  
    fg_data_pos2                            html  
    fg_data_pos30                           html  
    fg_extract_phenotypes                   html  
    fg_extract_raw                          html  
    fg_extract_samples                      html  
    fg_feat_cumsum                          html  
    fg_feat_edge_specenr                    html  
    fg_feat_mean_class                      html  
    fg_feat_node_prop                       html  
    fg_feat_node_specenr                    html  
    fg_feat_prop_edge                       html  
    fg_get_feature                          html  
    fg_get_feature_desc                     html  
    fg_get_feature_means                    html  
    fg_get_graph                            html  
    fg_get_markers                          html  
    fg_get_meta                             html  
    fg_get_summary                          html  
    fg_get_summary_desc                     html  
    fg_get_summary_index                    html  
    fg_get_summary_tables                   html  
    fg_gsub_ids                             html  
    fg_gsub_markers                         html  
    fg_load                                 html  
    fg_merge                                html  
    fg_merge_samples                        html  
    fg_plot                                 html  
    fg_plot_box                             html  
    fg_plot_pVSdiff                         html  
    fg_plot_qq                              html  
    fg_replace_meta                         html  
    fg_rm_feature                           html  
    fg_rm_summary                           html  
    fg_save                                 html  
    fg_save_plots                           html  
    fg_set_layout                           html  
    fg_summary                              html  
    flowGraph-class                         html  
    flowGraph                               html  
    flowGraphSubset                         html  
    flowGraphSubset_summary_adjust          html  
    flowGraphSubset_summary_pars            html  
    fpurrr_map                              html  
    get_child                               html  
    get_eprop                               html  
    get_paren                               html  
    get_phen_list                           html  
    get_phen_meta                           html  
    ggdf                                    html  
    loop_ind_f                              html  
    meandiff                                html  
    ms_create                               html  
    ms_psig                                 html  
    plot_gr                                 html  
    set_layout_graph                        html  
    summary_table                           html  
    test_c                                  html  
    time_output                             html  
    tstr                                    html  
** 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 'flowGraph' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowGraph' as flowGraph_1.0.0.zip
* DONE (flowGraph)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'flowGraph' 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(flowGraph)
> 
> test_check("flowGraph")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
   4.79    0.31    5.07


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(flowGraph)
> 
> test_check("flowGraph")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
   5.45    0.21    5.65

name	user	system	elapsed
cell_type_layers	0	0	0
fg_add_feature	0.26	0.00	0.27
fg_add_summary	0.7	0.0	0.7
fg_clean_phen	0	0	0
fg_clear_features	0.69	0.00	0.69
fg_clear_summary	0.30	0.00	0.29
fg_extract_phenotypes	0.22	0.00	0.22
fg_extract_raw	0.67	0.00	0.67
fg_extract_samples	0.22	0.00	0.22
fg_feat_cumsum	0.22	0.00	0.22
fg_feat_edge_specenr	0.26	0.00	0.27
fg_feat_mean_class	0.21	0.03	0.23
fg_feat_node_prop	0.21	0.00	0.22
fg_feat_node_specenr	0.29	0.00	0.28
fg_feat_prop_edge	0.23	0.00	0.24
fg_get_feature	0.22	0.00	0.22
fg_get_feature_desc	0.70	0.02	0.71
fg_get_feature_means	1.13	0.01	1.14
fg_get_graph	0.25	0.00	0.25
fg_get_markers	0.23	0.00	0.24
fg_get_meta	0.24	0.00	0.23
fg_get_summary	1.70	0.00	1.71
fg_get_summary_desc	0.84	0.03	0.87
fg_get_summary_index	1.58	0.00	1.58
fg_get_summary_tables	1.06	0.00	1.06
fg_gsub_ids	0.21	0.00	0.21
fg_gsub_markers	0.23	0.00	0.23
fg_load	37.39	0.36	37.81
fg_merge	0.24	0.00	0.24
fg_merge_samples	0.26	0.02	0.28
fg_plot	0.38	0.00	0.37
fg_plot_box	0.59	0.00	0.60
fg_plot_pVSdiff	0.36	0.00	0.36
fg_plot_qq	1.25	0.01	1.32
fg_replace_meta	0.27	0.00	0.27
fg_rm_feature	0.79	0.02	0.81
fg_rm_summary	0.35	0.00	0.34
fg_save	36.68	0.46	37.16
fg_save_plots	37.80	0.36	38.37
fg_set_layout	0.36	0.02	0.38
fg_summary	0.41	0.00	0.40
flowGraph-class	0	0	0
flowGraph	1.00	0.02	1.02
flowGraphSubset	0	0	0
flowGraphSubset_summary_adjust	0	0	0
flowGraphSubset_summary_pars	0	0	0
get_phen_list	0	0	0
get_phen_meta	0	0	0
ggdf	0.25	0.00	0.25
loop_ind_f	0	0	0
meandiff	0	0	0
plot_gr	1.39	0.01	1.40
set_layout_graph	0.44	0.00	0.44
summary_table	0	0	0
time_output	0	0	0
tstr	0	0	0

name	user	system	elapsed
cell_type_layers	0	0	0
fg_add_feature	0.29	0.00	0.30
fg_add_summary	0.83	0.02	0.85
fg_clean_phen	0	0	0
fg_clear_features	0.84	0.00	0.84
fg_clear_summary	0.34	0.00	0.34
fg_extract_phenotypes	0.27	0.00	0.27
fg_extract_raw	0.76	0.00	0.77
fg_extract_samples	0.27	0.00	0.27
fg_feat_cumsum	0.26	0.00	0.26
fg_feat_edge_specenr	0.31	0.00	0.31
fg_feat_mean_class	0.25	0.00	0.25
fg_feat_node_prop	0.27	0.00	0.27
fg_feat_node_specenr	0.31	0.00	0.31
fg_feat_prop_edge	0.42	0.00	0.42
fg_get_feature	0.30	0.02	0.32
fg_get_feature_desc	0.86	0.00	0.86
fg_get_feature_means	1.31	0.00	1.31
fg_get_graph	0.27	0.00	0.27
fg_get_markers	0.33	0.01	0.34
fg_get_meta	0.26	0.02	0.28
fg_get_summary	1.96	0.00	1.95
fg_get_summary_desc	0.90	0.04	0.96
fg_get_summary_index	1.77	0.00	1.76
fg_get_summary_tables	1.20	0.00	1.21
fg_gsub_ids	0.25	0.00	0.25
fg_gsub_markers	0.28	0.00	0.28
fg_load	36.75	0.44	37.22
fg_merge	0.25	0.02	0.26
fg_merge_samples	0.3	0.0	0.3
fg_plot	0.39	0.00	0.39
fg_plot_box	0.63	0.01	0.64
fg_plot_pVSdiff	0.37	0.02	0.39
fg_plot_qq	1.08	0.03	1.11
fg_replace_meta	0.25	0.00	0.25
fg_rm_feature	0.82	0.00	0.82
fg_rm_summary	0.36	0.01	0.37
fg_save	38.93	0.36	39.30
fg_save_plots	39.39	0.35	39.73
fg_set_layout	0.24	0.00	0.24
fg_summary	0.33	0.00	0.33
flowGraph-class	0	0	0
flowGraph	1.01	0.00	1.01
flowGraphSubset	0	0	0
flowGraphSubset_summary_adjust	0	0	0
flowGraphSubset_summary_pars	0	0	0
get_phen_list	0.02	0.00	0.02
get_phen_meta	0	0	0
ggdf	0.23	0.01	0.25
loop_ind_f	0	0	0
meandiff	0	0	0
plot_gr	1.16	0.02	1.17
set_layout_graph	0.23	0.01	0.25
summary_table	0	0	0
time_output	0	0	0
tstr	0	0	0

CHECK results for flowGraph on tokay2

Summary

Command output

Installation output

Tests output

Example timings