Multiple platform build/check report for BioC 3.11 - CHECK report for GeneAccord on tokay2

Package: GeneAccord

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAccord.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GeneAccord_1.6.0.tar.gz

StartedAt: 2020-10-17 04:17:05 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 04:22:49 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 344.4 seconds

RetCode: 0

Status: OK

CheckDir: GeneAccord.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAccord.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GeneAccord_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GeneAccord.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneAccord/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAccord' 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 'GeneAccord' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    extdata   2.1Mb
* 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
** 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-3.11-bioc/meat/GeneAccord.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/GeneAccord_1.6.0.tar.gz && rm -rf GeneAccord.buildbin-libdir && mkdir GeneAccord.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneAccord.buildbin-libdir GeneAccord_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL GeneAccord_1.6.0.zip && rm GeneAccord_1.6.0.tar.gz GeneAccord_1.6.0.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 2736k  100 2736k    0     0  23.7M      0 --:--:-- --:--:-- --:--:-- 25.4M

install for i386

* installing *source* package 'GeneAccord' ...
** 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 'GeneAccord'
    finding HTML links ... done
    GeneAccord                              html  
    all_genes_tbl                           html  
    avg_rates_m                             html  
    build_null_test_statistic               html  
    clone_tbl_all_pats_all_trees            html  
    compute_rates_clon_excl                 html  
    compute_test_stat_avg_rate              html  
    convert_ensembl_to_reactome_pw_tbl      html  
    create_ensembl_gene_tbl_hg              html  
    create_tbl_ent_clones                   html  
    create_tbl_tree_collection              html  
    ecdf_list                               html  
    ecdf_lr_test_clon_excl_avg_rate         html  
    ensembl_to_hgnc                         html  
    ensembl_to_reactome                     html  
    ensg_reactome_path_map                  html  
    ensmusg_reactome_path_map               html  
    extract_num_clones_tbl                  html  
    generate_ecdf_test_stat                 html  
    generate_test_stat_hist                 html  
    get_hist_clon_excl                      html  
    get_hist_clon_excl_this_pat_this_pair   html  
    get_rate_diff_branch_ent_pair           html  
    heatmap_clones_gene_pat                 html  
    hgnc_to_ensembl                         html  
    is_diff_branch_ent_pair                 html  
    list_of_clon_excl_all_pats              html  
    list_of_num_trees_all_pats              html  
    map_pairs_to_hgnc_symbols               html  
    merge_clones_identical_ents             html  
    pairs_in_patients_hist                  html  
    plot_ecdf_test_stat                     html  
    plot_rates_clon_excl                    html  
    take_pairs_and_get_patients             html  
    vis_pval_distr_num_pat                  html  
    write_res_pairs_to_disk                 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 'GeneAccord' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneAccord' as GeneAccord_1.6.0.zip
* DONE (GeneAccord)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'GeneAccord' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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("assertthat")
> 
> library("GeneAccord")
> # "When R CMD check runs tests, it sets R_TESTS. When the tests
> # themeselves run R CMD xxxx, as is the case with the tests in
> # devtools, having R_TESTS set causes errors because it confuses
> # the R subprocesses. Unsetting it here avoids those problems.
> #"R_TESTS" = "" "
> Sys.setenv("R_TESTS" = "")
> 
> test_check("GeneAccord")
== testthat results  ===========================================================
[ OK: 27 | SKIPPED: 6 | WARNINGS: 1 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
  18.73    0.75   22.67


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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("assertthat")
> 
> library("GeneAccord")
> # "When R CMD check runs tests, it sets R_TESTS. When the tests
> # themeselves run R CMD xxxx, as is the case with the tests in
> # devtools, having R_TESTS set causes errors because it confuses
> # the R subprocesses. Unsetting it here avoids those problems.
> #"R_TESTS" = "" "
> Sys.setenv("R_TESTS" = "")
> 
> test_check("GeneAccord")
== testthat results  ===========================================================
[ OK: 27 | SKIPPED: 6 | WARNINGS: 1 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
  18.39    0.48   22.20

name	user	system	elapsed
GeneAccord	1.93	0.02	1.94
build_null_test_statistic	1.61	0.00	1.61
compute_rates_clon_excl	0.2	0.0	0.2
compute_test_stat_avg_rate	0.04	0.00	0.03
convert_ensembl_to_reactome_pw_tbl	0.32	0.01	0.35
create_ensembl_gene_tbl_hg	0	0	0
create_tbl_ent_clones	0.03	0.00	0.03
create_tbl_tree_collection	0.33	0.02	0.35
ecdf_lr_test_clon_excl_avg_rate	0.66	0.00	0.65
ensembl_to_hgnc	0	0	0
ensembl_to_reactome	0.01	0.01	0.03
extract_num_clones_tbl	0.02	0.00	0.02
generate_ecdf_test_stat	0.54	0.00	0.55
generate_test_stat_hist	0.88	0.00	0.87
get_hist_clon_excl	0.61	0.00	0.61
get_hist_clon_excl_this_pat_this_pair	0.02	0.00	0.01
get_rate_diff_branch_ent_pair	0.42	0.00	0.42
heatmap_clones_gene_pat	0.59	0.00	0.60
hgnc_to_ensembl	0	0	0
is_diff_branch_ent_pair	0.02	0.00	0.01
map_pairs_to_hgnc_symbols	0	0	0
merge_clones_identical_ents	0.05	0.00	0.05
pairs_in_patients_hist	0.04	0.00	0.05
plot_ecdf_test_stat	0.21	0.00	0.20
plot_rates_clon_excl	0.2	0.0	0.2
take_pairs_and_get_patients	0.22	0.00	0.22
vis_pval_distr_num_pat	0.03	0.00	0.03
write_res_pairs_to_disk	0.00	0.02	0.10

name	user	system	elapsed
GeneAccord	2.20	0.02	2.22
build_null_test_statistic	1.56	0.00	1.56
compute_rates_clon_excl	0.32	0.00	0.31
compute_test_stat_avg_rate	0.03	0.00	0.04
convert_ensembl_to_reactome_pw_tbl	0.45	0.01	0.46
create_ensembl_gene_tbl_hg	0	0	0
create_tbl_ent_clones	0.05	0.00	0.05
create_tbl_tree_collection	0.39	0.00	0.39
ecdf_lr_test_clon_excl_avg_rate	0.98	0.00	0.98
ensembl_to_hgnc	0	0	0
ensembl_to_reactome	0.03	0.00	0.03
extract_num_clones_tbl	0.03	0.00	0.03
generate_ecdf_test_stat	0.75	0.00	0.75
generate_test_stat_hist	0.86	0.00	0.86
get_hist_clon_excl	0.71	0.00	0.70
get_hist_clon_excl_this_pat_this_pair	0.01	0.00	0.02
get_rate_diff_branch_ent_pair	0.59	0.00	0.59
heatmap_clones_gene_pat	0.75	0.00	0.75
hgnc_to_ensembl	0	0	0
is_diff_branch_ent_pair	0.02	0.00	0.02
map_pairs_to_hgnc_symbols	0.02	0.00	0.01
merge_clones_identical_ents	0.04	0.00	0.05
pairs_in_patients_hist	0.07	0.00	0.06
plot_ecdf_test_stat	0.21	0.00	0.22
plot_rates_clon_excl	0.29	0.00	0.28
take_pairs_and_get_patients	0.29	0.00	0.30
vis_pval_distr_num_pat	0.03	0.00	0.03
write_res_pairs_to_disk	0	0	0

CHECK report for GeneAccord on tokay2

Summary

Command output

Installation output

Tests output

Example timings