Multiple platform build/check report for BioC 3.8 - CHECK report for DeepBlueR on tokay1

Package: DeepBlueR

Version: 1.8.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeepBlueR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DeepBlueR_1.8.1.tar.gz

StartedAt: 2019-04-13 01:40:38 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 01:47:35 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 416.6 seconds

RetCode: 0

Status: OK

CheckDir: DeepBlueR.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeepBlueR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DeepBlueR_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DeepBlueR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DeepBlueR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeepBlueR' version '1.8.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'DeepBlueR' 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 ... NOTE
prepare_Rd: deepblue_enrich_regions_fast.Rd:35-38: Dropping empty section \examples
* 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 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-3.8-bioc/meat/DeepBlueR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DeepBlueR_1.8.1.tar.gz && rm -rf DeepBlueR.buildbin-libdir && mkdir DeepBlueR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeepBlueR.buildbin-libdir DeepBlueR_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DeepBlueR_1.8.1.zip && rm DeepBlueR_1.8.1.tar.gz DeepBlueR_1.8.1.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  521k  100  521k    0     0  11.7M      0 --:--:-- --:--:-- --:--:-- 12.7M

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'DeepBlueR/vignettes/DeepBlueR.Rmd' to 'DeepBlueR/README.md'
* installing *source* package 'DeepBlueR' ...
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Called method: deepblue_list_column_types
Reported status was: okay
Called method: deepblue_info
Reported status was: okay
** help
*** installing help indices
  converting help for package 'DeepBlueR'
    finding HTML links ... done
    DeepBlueCommand-class                   html  
    deepblue_aggregate                      html  
    deepblue_batch_export_results           html  
    deepblue_binning                        html  
    deepblue_cache_status                   html  
    deepblue_cancel_request                 html  
    deepblue_chromosomes                    html  
    deepblue_clear_cache                    html  
    deepblue_collection_experiments_count   html  
    deepblue_column_types                   html  
    deepblue_commands                       html  
    deepblue_convert_to_df                  html  
    deepblue_convert_to_grange              html  
    deepblue_count_gene_ontology_terms      html  
    deepblue_count_regions                  html  
    deepblue_coverage                       html  
    deepblue_delete_request_from_cache      html  
    deepblue_diff                           html  
    deepblue_distinct_column_values         html  
    deepblue_download_request_data-DeepBlueCommand-method
                                            html  
    deepblue_download_request_data          html  
    deepblue_echo                           html  
    deepblue_enrich_regions_fast            html  
    deepblue_enrich_regions_go_terms        html  
    deepblue_enrich_regions_overlap         html  
    deepblue_export_bed                     html  
    deepblue_export_meta_data               html  
    deepblue_export_tab                     html  
    deepblue_extend                         html  
    deepblue_extract_ids                    html  
    deepblue_extract_names                  html  
    deepblue_faceting_experiments           html  
    deepblue_filter_regions                 html  
    deepblue_find_motif                     html  
    deepblue_flank                          html  
    deepblue_format_object_size             html  
    deepblue_get_biosource_children         html  
    deepblue_get_biosource_parents          html  
    deepblue_get_biosource_related          html  
    deepblue_get_biosource_synonyms         html  
    deepblue_get_db                         html  
    deepblue_get_experiments_by_query       html  
    deepblue_get_regions                    html  
    deepblue_get_request_data               html  
    deepblue_info                           html  
    deepblue_input_regions                  html  
    deepblue_intersection                   html  
    deepblue_is_biosource                   html  
    deepblue_liftover                       html  
    deepblue_list_annotations               html  
    deepblue_list_biosources                html  
    deepblue_list_cached_requests           html  
    deepblue_list_column_types              html  
    deepblue_list_epigenetic_marks          html  
    deepblue_list_experiments               html  
    deepblue_list_expressions               html  
    deepblue_list_gene_models               html  
    deepblue_list_genes                     html  
    deepblue_list_genomes                   html  
    deepblue_list_in_use                    html  
    deepblue_list_projects                  html  
    deepblue_list_recent_experiments        html  
    deepblue_list_requests                  html  
    deepblue_list_samples                   html  
    deepblue_list_similar_biosources        html  
    deepblue_list_similar_epigenetic_marks
                                            html  
    deepblue_list_similar_experiments       html  
    deepblue_list_similar_genomes           html  
    deepblue_list_similar_projects          html  
    deepblue_list_similar_techniques        html  
    deepblue_list_techniques                html  
    deepblue_merge_queries                  html  
    deepblue_meta_data_to_table             html  
    deepblue_name_to_id                     html  
    deepblue_options                        html  
    deepblue_overlap                        html  
    deepblue_parse_gtf                      html  
    deepblue_preview_experiment             html  
    deepblue_query_cache                    html  
    deepblue_query_experiment_type          html  
    deepblue_reset_options                  html  
    deepblue_score_matrix                   html  
    deepblue_search                         html  
    deepblue_select_annotations             html  
    deepblue_select_column                  html  
    deepblue_select_experiments             html  
    deepblue_select_expressions             html  
    deepblue_select_genes                   html  
    deepblue_select_regions                 html  
    deepblue_switch_get_request_data        html  
    deepblue_tiling_regions                 html  
    deepblue_wait_request                   html  
    show-DeepBlueCommand-method             html  
    xml.rpc                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'DeepBlueR/vignettes/DeepBlueR.Rmd' to 'DeepBlueR/README.md'
* installing *source* package 'DeepBlueR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeepBlueR' as DeepBlueR_1.8.1.zip
* DONE (DeepBlueR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DeepBlueR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

name	user	system	elapsed
deepblue_aggregate	0.09	0.03	0.78
deepblue_batch_export_results	0.47	0.24	4.24
deepblue_binning	0.05	0.00	0.50
deepblue_cache_status	0	0	0
deepblue_cancel_request	0.03	0.00	0.25
deepblue_chromosomes	0.08	0.00	0.30
deepblue_clear_cache	0	0	0
deepblue_collection_experiments_count	0.11	0.02	0.59
deepblue_commands	0.11	0.00	0.72
deepblue_count_gene_ontology_terms	0.11	0.03	0.61
deepblue_count_regions	0.04	0.01	0.50
deepblue_coverage	0.06	0.00	0.50
deepblue_delete_request_from_cache	0	0	0
deepblue_diff	0.16	0.11	1.53
deepblue_distinct_column_values	0.06	0.00	0.52
deepblue_download_request_data	0.93	0.14	2.93
deepblue_echo	0.03	0.00	0.24
deepblue_enrich_regions_go_terms	0.06	0.00	0.73
deepblue_enrich_regions_overlap	0.62	0.00	3.88
deepblue_export_bed	0.24	0.18	2.65
deepblue_export_meta_data	0.06	0.00	0.39
deepblue_export_tab	0.11	0.03	1.04
deepblue_extend	0.04	0.00	0.50
deepblue_extract_ids	0	0	0
deepblue_extract_names	0	0	0
deepblue_faceting_experiments	0.05	0.00	0.49
deepblue_filter_regions	0.05	0.00	0.26
deepblue_find_motif	0.03	0.00	0.24
deepblue_flank	0.06	0.00	0.50
deepblue_get_biosource_children	0.00	0.00	0.23
deepblue_get_biosource_parents	0.03	0.00	0.25
deepblue_get_biosource_related	0.02	0.00	0.25
deepblue_get_biosource_synonyms	0.01	0.00	0.52
deepblue_get_experiments_by_query	0.03	0.00	0.23
deepblue_get_regions	0.04	0.00	1.00
deepblue_get_request_data	0.07	0.00	1.00
deepblue_info	0.03	0.00	0.25
deepblue_input_regions	0.02	0.00	0.25
deepblue_intersection	0.09	0.00	0.74
deepblue_is_biosource	0.04	0.00	0.23
deepblue_liftover	0.53	0.22	3.53
deepblue_list_annotations	0.01	0.00	0.25
deepblue_list_biosources	0.02	0.00	0.24
deepblue_list_cached_requests	0	0	0
deepblue_list_column_types	0.09	0.00	0.40
deepblue_list_epigenetic_marks	0.49	0.00	1.05
deepblue_list_experiments	0.15	0.00	0.64
deepblue_list_expressions	0.11	0.00	0.42
deepblue_list_gene_models	0.02	0.00	0.24
deepblue_list_genes	0.28	0.00	0.97
deepblue_list_genomes	0.01	0.00	0.23
deepblue_list_in_use	0.46	0.00	1.50
deepblue_list_projects	0.01	0.00	0.23
deepblue_list_recent_experiments	0.05	0.00	0.27
deepblue_list_requests	0.02	0.00	0.23
deepblue_list_samples	0.15	0.00	0.61
deepblue_list_similar_biosources	0.03	0.00	0.43
deepblue_list_similar_epigenetic_marks	0.02	0.00	0.25
deepblue_list_similar_experiments	0.03	0.00	0.85
deepblue_list_similar_genomes	0.02	0.00	0.22
deepblue_list_similar_projects	0.03	0.00	0.30
deepblue_list_similar_techniques	0.01	0.00	0.23
deepblue_list_techniques	0.05	0.00	0.27
deepblue_merge_queries	0.09	0.00	0.73
deepblue_meta_data_to_table	0.14	0.00	0.66
deepblue_name_to_id	0.05	0.00	0.74
deepblue_overlap	0.08	0.00	0.71
deepblue_preview_experiment	0.01	0.00	0.25
deepblue_query_cache	0.11	0.02	0.99
deepblue_query_experiment_type	0.03	0.01	0.48
deepblue_reset_options	0	0	0
deepblue_score_matrix	0.04	0.00	0.49
deepblue_search	0.04	0.00	0.61
deepblue_select_annotations	0.03	0.00	0.25
deepblue_select_column	0.27	0.00	0.87
deepblue_select_experiments	0.05	0.00	0.27
deepblue_select_expressions	0.03	0.00	0.34
deepblue_select_genes	0.01	0.00	0.34
deepblue_select_regions	0.05	0.00	0.27
deepblue_tiling_regions	0.02	0.00	0.23

name	user	system	elapsed
deepblue_aggregate	0.08	0.01	0.75
deepblue_batch_export_results	0.48	0.11	3.75
deepblue_binning	0.05	0.00	0.49
deepblue_cache_status	0	0	0
deepblue_cancel_request	0.03	0.00	0.25
deepblue_chromosomes	0.08	0.00	0.30
deepblue_clear_cache	0	0	0
deepblue_collection_experiments_count	0.12	0.00	0.60
deepblue_commands	0.13	0.02	0.75
deepblue_count_gene_ontology_terms	0.12	0.00	0.58
deepblue_count_regions	0.05	0.00	0.49
deepblue_coverage	0.03	0.01	0.47
deepblue_delete_request_from_cache	0	0	0
deepblue_diff	0.12	0.06	0.84
deepblue_distinct_column_values	0.07	0.00	0.50
deepblue_download_request_data	0.22	0.10	2.22
deepblue_echo	0.01	0.00	0.23
deepblue_enrich_regions_go_terms	0.10	0.00	0.72
deepblue_enrich_regions_overlap	0.79	0.00	4.03
deepblue_export_bed	0.27	0.06	2.63
deepblue_export_meta_data	0.11	0.00	0.44
deepblue_export_tab	0.15	0.00	1.04
deepblue_extend	0.06	0.00	0.50
deepblue_extract_ids	0	0	0
deepblue_extract_names	0	0	0
deepblue_faceting_experiments	0.05	0.00	0.50
deepblue_filter_regions	0.03	0.00	0.26
deepblue_find_motif	0.03	0.02	0.25
deepblue_flank	0.03	0.00	0.50
deepblue_get_biosource_children	0.02	0.00	0.25
deepblue_get_biosource_parents	0.03	0.00	0.25
deepblue_get_biosource_related	0.03	0.00	0.25
deepblue_get_biosource_synonyms	0.03	0.00	0.25
deepblue_get_experiments_by_query	0.02	0.00	0.24
deepblue_get_regions	0.03	0.00	0.76
deepblue_get_request_data	0.09	0.00	0.99
deepblue_info	0.03	0.00	0.25
deepblue_input_regions	0.02	0.00	0.26
deepblue_intersection	0.05	0.00	0.74
deepblue_is_biosource	0.03	0.00	0.25
deepblue_liftover	1.33	0.12	4.08
deepblue_list_annotations	0.03	0.00	0.26
deepblue_list_biosources	0.00	0.00	0.24
deepblue_list_cached_requests	0	0	0
deepblue_list_column_types	0.07	0.00	0.40
deepblue_list_epigenetic_marks	0.58	0.02	1.10
deepblue_list_experiments	0.22	0.00	0.67
deepblue_list_expressions	0.14	0.04	0.51
deepblue_list_gene_models	0.03	0.00	0.24
deepblue_list_genes	0.28	0.05	0.95
deepblue_list_genomes	0.02	0.00	0.24
deepblue_list_in_use	0.52	0.00	1.54
deepblue_list_projects	0.01	0.00	0.25
deepblue_list_recent_experiments	0.05	0.00	0.27
deepblue_list_requests	0.03	0.00	0.23
deepblue_list_samples	0.19	0.00	0.64
deepblue_list_similar_biosources	0.03	0.00	0.42
deepblue_list_similar_epigenetic_marks	0.03	0.00	0.27
deepblue_list_similar_experiments	0.02	0.00	0.83
deepblue_list_similar_genomes	0.03	0.00	0.26
deepblue_list_similar_projects	0.03	0.00	0.24
deepblue_list_similar_techniques	0.03	0.00	0.23
deepblue_list_techniques	0.01	0.00	0.25
deepblue_merge_queries	0.08	0.02	0.74
deepblue_meta_data_to_table	0.14	0.00	0.68
deepblue_name_to_id	0.07	0.00	0.74
deepblue_overlap	0.07	0.00	0.72
deepblue_preview_experiment	0.02	0.00	0.23
deepblue_query_cache	0.11	0.00	1.05
deepblue_query_experiment_type	0.06	0.00	0.50
deepblue_reset_options	0	0	0
deepblue_score_matrix	0.06	0.00	0.50
deepblue_search	0.05	0.00	0.59
deepblue_select_annotations	0.05	0.00	0.25
deepblue_select_column	0.50	0.00	1.14
deepblue_select_experiments	0.03	0.00	0.25
deepblue_select_expressions	0.01	0.00	0.36
deepblue_select_genes	0.04	0.00	0.35
deepblue_select_regions	0.04	0.00	0.26
deepblue_tiling_regions	0.03	0.00	0.24

CHECK report for DeepBlueR on tokay1

Summary

Command output

Installation output

Tests output

Example timings