Package: DeepBlueR

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DeepBlueR_1.6.0.tar.gz

StartedAt: 2018-10-16 20:51:05 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:56:11 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 306.1 seconds

RetCode: 0

Status:  OK

CheckDir: DeepBlueR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DeepBlueR_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeepBlueR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepBlueR’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
deepblue_enrich_regions_overlap 0.709  0.036   6.649
* 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DeepBlueR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DeepBlueR)

name	user	system	elapsed
deepblue_aggregate	0.112	0.009	3.692
deepblue_batch_export_results	0.394	0.018	4.193
deepblue_binning	0.049	0.002	0.851
deepblue_cache_status	0.004	0.001	0.005
deepblue_cancel_request	0.022	0.001	0.244
deepblue_chromosomes	0.055	0.002	0.279
deepblue_clear_cache	0.002	0.000	0.003
deepblue_collection_experiments_count	0.122	0.006	0.568
deepblue_commands	0.152	0.021	0.723
deepblue_count_gene_ontology_terms	0.486	0.034	0.956
deepblue_count_regions	0.044	0.002	0.511
deepblue_coverage	0.050	0.002	0.936
deepblue_delete_request_from_cache	0.003	0.001	0.005
deepblue_diff	0.125	0.017	0.590
deepblue_distinct_column_values	0.046	0.002	0.830
deepblue_download_request_data	0.771	0.011	2.631
deepblue_echo	0.015	0.001	0.236
deepblue_enrich_regions_go_terms	0.065	0.003	3.508
deepblue_enrich_regions_overlap	0.709	0.036	6.649
deepblue_export_bed	0.238	0.036	4.931
deepblue_export_meta_data	0.100	0.014	0.442
deepblue_export_tab	0.123	0.018	3.699
deepblue_extend	0.059	0.009	0.511
deepblue_extract_ids	0.002	0.000	0.002
deepblue_extract_names	0.001	0.000	0.002
deepblue_faceting_experiments	0.038	0.005	0.509
deepblue_filter_regions	0.031	0.005	2.587
deepblue_find_motif	0.034	0.005	0.259
deepblue_flank	0.061	0.008	0.514
deepblue_get_biosource_children	0.025	0.003	0.252
deepblue_get_biosource_parents	0.021	0.003	0.245
deepblue_get_biosource_related	0.023	0.003	0.253
deepblue_get_biosource_synonyms	0.022	0.004	0.246
deepblue_get_experiments_by_query	0.022	0.003	0.258
deepblue_get_regions	0.071	0.007	0.936
deepblue_get_request_data	0.089	0.003	1.393
deepblue_info	0.043	0.002	0.268
deepblue_input_regions	0.024	0.001	0.489
deepblue_intersection	0.080	0.003	0.928
deepblue_is_biosource	0.019	0.001	0.241
deepblue_liftover	0.484	0.056	3.640
deepblue_list_annotations	0.027	0.002	0.248
deepblue_list_biosources	0.024	0.001	0.243
deepblue_list_cached_requests	0.003	0.001	0.004
deepblue_list_column_types	0.058	0.001	0.391
deepblue_list_epigenetic_marks	0.475	0.005	1.037
deepblue_list_experiments	0.202	0.001	0.659
deepblue_list_expressions	0.145	0.001	0.477
deepblue_list_gene_models	0.014	0.001	0.235
deepblue_list_genes	0.294	0.006	0.959
deepblue_list_genomes	0.022	0.001	0.247
deepblue_list_in_use	0.526	0.027	1.632
deepblue_list_projects	0.022	0.001	0.245
deepblue_list_recent_experiments	0.034	0.001	0.256
deepblue_list_requests	0.015	0.000	0.237
deepblue_list_samples	0.165	0.012	0.635
deepblue_list_similar_biosources	0.033	0.001	0.385
deepblue_list_similar_epigenetic_marks	0.030	0.001	0.257
deepblue_list_similar_experiments	0.022	0.001	0.821
deepblue_list_similar_genomes	0.021	0.001	0.243
deepblue_list_similar_projects	0.023	0.001	0.244
deepblue_list_similar_techniques	0.024	0.001	0.245
deepblue_list_techniques	0.035	0.002	0.257
deepblue_merge_queries	0.075	0.003	0.769
deepblue_meta_data_to_table	0.119	0.004	0.673
deepblue_name_to_id	0.062	0.003	0.913
deepblue_overlap	0.080	0.003	1.262
deepblue_preview_experiment	0.021	0.001	0.253
deepblue_query_cache	0.088	0.003	1.002
deepblue_query_experiment_type	0.062	0.002	2.836
deepblue_reset_options	0.001	0.000	0.001
deepblue_score_matrix	0.050	0.001	0.876
deepblue_search	0.064	0.002	0.595
deepblue_select_annotations	0.032	0.001	0.259
deepblue_select_column	0.419	0.005	0.988
deepblue_select_experiments	0.021	0.001	0.257
deepblue_select_expressions	0.032	0.001	0.369
deepblue_select_genes	0.031	0.001	0.359
deepblue_select_regions	0.033	0.001	2.314
deepblue_tiling_regions	0.024	0.001	0.244