Multiple platform build/check report for BioC 3.14 - CHECK results for CIMICE 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: CIMICE

Version: 1.2.1

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CIMICE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CIMICE_1.2.1.tar.gz

StartedAt: 2022-04-12 17:18:58 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 17:21:11 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 132.1 seconds

RetCode: 0

Status: OK

CheckDir: CIMICE.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CIMICE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CIMICE_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CIMICE.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 'CIMICE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CIMICE' version '1.2.1'
* 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 ... NOTE
Found the following hidden files and directories:
  .git.bfg-report
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'CIMICE' 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 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/CIMICE.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CIMICE_1.2.1.tar.gz && rm -rf CIMICE.buildbin-libdir && mkdir CIMICE.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CIMICE.buildbin-libdir CIMICE_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CIMICE_1.2.1.zip && rm CIMICE_1.2.1.tar.gz CIMICE_1.2.1.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  500k  100  500k    0     0   888k      0 --:--:-- --:--:-- --:--:--  890k

install for i386

* installing *source* package 'CIMICE' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CIMICE'
    finding HTML links ... done
    CIMICE                                  html  
    annotate_mutational_matrix              html  
    binary_radix_sort                       html  
    build_subset_graph                      html  
    build_topology_subset                   html  
    chunk_reader                            html  
    compact_dataset                         html  
    computeDWNW                             html  
    computeDWNW_aux                         html  
    computeUPW                              html  
    computeUPW_aux                          html  
    compute_weights_default                 html  
    corrplot_from_mutational_matrix         html  
    corrplot_genes                          html  
    corrplot_samples                        html  
    dataset_preprocessing                   html  
    dataset_preprocessing_population        html  
    draw_ggraph                             html  
    draw_networkD3                          html  
    draw_visNetwork                         html  
    example_dataset                         html  
    example_dataset_withFreqs               html  
    finalize_generator                      html  
    fix_clonal_genotype                     html  
    format_labels                           html  
    gene_mutations_hist                     html  
    get_no_of_children                      html  
    graph_non_transitive_subset_topology    html  
    make_dataset                            html  
    make_generator_stub                     html  
    make_labels                             html  
    normalizeDWNW                           html  
    normalizeUPW                            html  
    perturb_dataset                         html  
    plot_generator                          html  
    prepare_generator_edge_set_command      html  
    prepare_labels                          html  
    quick_run                               html  
    read                                    html  
    read_CAPRI                              html  
    read_CAPRI_string                       html  
    read_CAPRIpop                           html  
    read_CAPRIpop_string                    html  
    read_MAF                                html  
    read_matrix                             html  
    remove_transitive_edges                 html  
    sample_mutations_hist                   html  
    select_genes_on_mutations               html  
    select_samples_on_mutations             html  
    set_generator_edges                     html  
    simulate_generator                      html  
    to_dot                                  html  
    update_df                               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 'CIMICE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CIMICE' as CIMICE_1.2.1.zip
* DONE (CIMICE)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CIMICE' 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(CIMICE)
> 
> test_check("CIMICE")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   3.03    0.29    3.29


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(CIMICE)
> 
> test_check("CIMICE")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   3.42    0.14    3.54

name	user	system	elapsed
annotate_mutational_matrix	0.03	0.00	0.03
binary_radix_sort	0.03	0.00	0.04
build_subset_graph	0.08	0.00	0.08
build_topology_subset	0.03	0.02	0.05
chunk_reader	0.00	0.00	0.04
compact_dataset	0.03	0.00	0.03
computeDWNW	0.11	0.00	0.11
computeUPW	0.11	0.00	0.11
compute_weights_default	0.11	0.00	0.11
corrplot_from_mutational_matrix	0.45	0.01	0.47
corrplot_genes	0.44	0.02	0.45
corrplot_samples	0.18	0.03	0.22
dataset_preprocessing	0.07	0.00	0.07
dataset_preprocessing_population	0.03	0.00	0.03
draw_ggraph	0.27	0.08	0.35
draw_networkD3	0.23	0.00	0.28
draw_visNetwork	0.11	0.01	0.86
example_dataset	0.02	0.00	0.01
example_dataset_withFreqs	0.01	0.00	0.02
finalize_generator	0.43	0.02	0.45
fix_clonal_genotype	0.06	0.00	0.06
format_labels	0	0	0
gene_mutations_hist	0.19	0.00	0.19
get_no_of_children	0.09	0.00	0.09
graph_non_transitive_subset_topology	0.06	0.00	0.07
make_dataset	0	0	0
make_generator_stub	0.24	0.00	0.23
make_labels	0.04	0.00	0.05
normalizeDWNW	0.10	0.00	0.09
normalizeUPW	0.08	0.00	0.08
perturb_dataset	0.19	0.01	0.20
plot_generator	0.5	0.0	0.5
prepare_generator_edge_set_command	0.25	0.00	0.25
prepare_labels	0.03	0.00	0.03
quick_run	0.06	0.00	0.06
read	1.29	0.21	1.59
read_CAPRI	1.36	0.15	1.52
read_CAPRI_string	0	0	0
read_CAPRIpop	0	0	0
read_CAPRIpop_string	0.02	0.00	0.01
read_MAF	0.19	0.03	0.22
read_matrix	0.01	0.00	0.02
remove_transitive_edges	0	0	0
sample_mutations_hist	0.14	0.00	0.14
select_genes_on_mutations	0.03	0.00	0.03
select_samples_on_mutations	0.05	0.00	0.05
set_generator_edges	0.2	0.0	0.2
simulate_generator	0.13	0.02	0.14
to_dot	0.06	0.00	0.06
update_df	0.03	0.00	0.03

name	user	system	elapsed
annotate_mutational_matrix	0.02	0.00	0.02
binary_radix_sort	0.05	0.00	0.05
build_subset_graph	0.06	0.01	0.08
build_topology_subset	0.05	0.00	0.05
chunk_reader	0.02	0.00	0.01
compact_dataset	0.01	0.00	0.02
computeDWNW	0.08	0.00	0.08
computeUPW	0.08	0.00	0.07
compute_weights_default	0.08	0.00	0.08
corrplot_from_mutational_matrix	0.34	0.00	0.35
corrplot_genes	0.42	0.00	0.42
corrplot_samples	0.13	0.02	0.14
dataset_preprocessing	0.01	0.01	0.03
dataset_preprocessing_population	0.03	0.00	0.03
draw_ggraph	0.25	0.03	0.28
draw_networkD3	0.16	0.00	0.16
draw_visNetwork	0.08	0.02	0.20
example_dataset	0.01	0.00	0.02
example_dataset_withFreqs	0.02	0.00	0.01
finalize_generator	0.42	0.00	0.42
fix_clonal_genotype	0.05	0.00	0.05
format_labels	0	0	0
gene_mutations_hist	0.15	0.01	0.17
get_no_of_children	0.08	0.00	0.08
graph_non_transitive_subset_topology	0.07	0.00	0.06
make_dataset	0	0	0
make_generator_stub	0.20	0.02	0.22
make_labels	0.06	0.00	0.07
normalizeDWNW	0.08	0.00	0.07
normalizeUPW	0.05	0.00	0.05
perturb_dataset	0.14	0.00	0.14
plot_generator	0.39	0.01	0.40
prepare_generator_edge_set_command	0.24	0.00	0.23
prepare_labels	0.04	0.00	0.05
quick_run	0.07	0.00	0.06
read	0.79	0.11	0.91
read_CAPRI	0.91	0.28	1.19
read_CAPRI_string	0.02	0.00	0.01
read_CAPRIpop	0	0	0
read_CAPRIpop_string	0	0	0
read_MAF	0.21	0.03	0.25
read_matrix	0	0	0
remove_transitive_edges	0	0	0
sample_mutations_hist	0.16	0.02	0.17
select_genes_on_mutations	0.03	0.00	0.03
select_samples_on_mutations	0.05	0.00	0.05
set_generator_edges	0.22	0.00	0.22
simulate_generator	0.24	0.00	0.23
to_dot	0.08	0.00	0.08
update_df	0.03	0.00	0.03

CHECK results for CIMICE on tokay2

Summary

Command output

Installation output

Tests output

Example timings