Package: DeepBlueR

Version: 1.8.1

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_1.8.1.tar.gz

StartedAt: 2019-04-15 23:24:53 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:29:36 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 283.6 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_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.1’
* 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
* 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-3.8-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	0.077	0.010	0.789
deepblue_batch_export_results	0.380	0.028	3.062
deepblue_binning	0.054	0.001	0.563
deepblue_cache_status	0.003	0.000	0.004
deepblue_cancel_request	0.019	0.001	0.268
deepblue_chromosomes	0.067	0.002	0.297
deepblue_clear_cache	0.001	0.001	0.002
deepblue_collection_experiments_count	0.138	0.016	0.621
deepblue_commands	0.515	0.820	0.674
deepblue_count_gene_ontology_terms	0.136	0.033	0.638
deepblue_count_regions	0.453	0.866	0.545
deepblue_coverage	0.037	0.005	0.519
deepblue_delete_request_from_cache	0.002	0.001	0.003
deepblue_diff	0.222	0.026	0.725
deepblue_distinct_column_values	0.044	0.002	0.522
deepblue_download_request_data	0.788	0.010	2.253
deepblue_echo	0.012	0.000	0.234
deepblue_enrich_regions_go_terms	0.073	0.002	0.782
deepblue_enrich_regions_overlap	0.683	0.030	4.318
deepblue_export_bed	0.239	0.037	2.174
deepblue_export_meta_data	0.102	0.016	0.487
deepblue_export_tab	0.124	0.017	1.100
deepblue_extend	0.058	0.009	0.542
deepblue_extract_ids	0.002	0.000	0.002
deepblue_extract_names	0.001	0.001	0.001
deepblue_faceting_experiments	0.039	0.006	0.558
deepblue_filter_regions	0.030	0.005	0.290
deepblue_find_motif	0.032	0.005	0.263
deepblue_flank	0.059	0.009	0.552
deepblue_get_biosource_children	0.023	0.004	0.292
deepblue_get_biosource_parents	0.018	0.003	0.273
deepblue_get_biosource_related	0.022	0.004	0.343
deepblue_get_biosource_synonyms	0.019	0.003	0.989
deepblue_get_experiments_by_query	0.020	0.003	0.281
deepblue_get_regions	0.047	0.007	0.551
deepblue_get_request_data	0.128	0.005	1.032
deepblue_info	0.041	0.004	0.271
deepblue_input_regions	0.019	0.001	0.278
deepblue_intersection	0.069	0.003	0.766
deepblue_is_biosource	0.015	0.001	0.237
deepblue_liftover	0.506	0.046	3.075
deepblue_list_annotations	0.029	0.001	0.253
deepblue_list_biosources	0.017	0.001	0.240
deepblue_list_cached_requests	0.002	0.001	0.003
deepblue_list_column_types	0.077	0.014	0.440
deepblue_list_epigenetic_marks	0.810	0.859	1.001
deepblue_list_experiments	0.841	0.765	0.608
deepblue_list_expressions	0.539	0.885	0.496
deepblue_list_gene_models	0.444	0.861	0.267
deepblue_list_genes	0.329	0.029	1.068
deepblue_list_genomes	0.431	0.821	0.266
deepblue_list_in_use	0.467	0.026	1.586
deepblue_list_projects	0.689	0.754	0.298
deepblue_list_recent_experiments	0.022	0.000	0.247
deepblue_list_requests	0.012	0.000	0.236
deepblue_list_samples	0.156	0.010	0.633
deepblue_list_similar_biosources	0.028	0.002	0.433
deepblue_list_similar_epigenetic_marks	0.029	0.001	0.269
deepblue_list_similar_experiments	0.018	0.001	0.843
deepblue_list_similar_genomes	0.022	0.001	0.271
deepblue_list_similar_projects	0.019	0.001	0.270
deepblue_list_similar_techniques	0.022	0.001	0.244
deepblue_list_techniques	0.035	0.002	0.258
deepblue_merge_queries	0.066	0.003	0.794
deepblue_meta_data_to_table	0.132	0.004	0.691
deepblue_name_to_id	0.061	0.003	0.754
deepblue_overlap	0.073	0.003	0.796
deepblue_preview_experiment	0.016	0.001	0.250
deepblue_query_cache	0.089	0.004	1.067
deepblue_query_experiment_type	0.062	0.002	0.569
deepblue_reset_options	0.000	0.000	0.001
deepblue_score_matrix	0.051	0.002	0.528
deepblue_search	0.047	0.002	0.627
deepblue_select_annotations	0.023	0.001	0.247
deepblue_select_column	0.487	0.053	1.153
deepblue_select_experiments	0.416	0.861	0.248
deepblue_select_expressions	0.021	0.001	0.355
deepblue_select_genes	0.024	0.001	0.355
deepblue_select_regions	0.040	0.001	0.296
deepblue_tiling_regions	0.021	0.001	0.273