Package: DeepBlueR

Version: 1.9.0

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_1.9.0.tar.gz

StartedAt: 2019-04-07 00:31:23 -0400 (Sun, 07 Apr 2019)

EndedAt: 2019-04-07 00:36:51 -0400 (Sun, 07 Apr 2019)

EllapsedTime: 328.1 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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DeepBlueR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.9.0’
* 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
* 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-3.9-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/3.6/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	0.096	0.014	0.838
deepblue_batch_export_results	0.960	0.030	3.715
deepblue_binning	0.054	0.002	0.558
deepblue_cache_status	0.003	0.001	0.004
deepblue_cancel_request	0.019	0.001	0.259
deepblue_chromosomes	0.112	0.057	0.322
deepblue_clear_cache	0.006	0.010	0.003
deepblue_collection_experiments_count	0.452	0.636	1.169
deepblue_commands	0.587	0.621	1.215
deepblue_count_gene_ontology_terms	0.940	0.557	1.222
deepblue_count_regions	0.453	0.614	0.516
deepblue_coverage	0.034	0.002	0.519
deepblue_delete_request_from_cache	0.003	0.001	0.004
deepblue_diff	0.774	0.917	0.660
deepblue_distinct_column_values	0.242	0.277	0.521
deepblue_download_request_data	0.220	0.013	1.744
deepblue_echo	0.017	0.001	0.259
deepblue_enrich_regions_go_terms	0.071	0.003	0.801
deepblue_enrich_regions_overlap	1.879	1.331	4.335
deepblue_export_bed	0.262	0.014	2.258
deepblue_export_meta_data	0.226	0.115	0.483
deepblue_export_tab	0.444	0.388	1.086
deepblue_extend	0.057	0.002	0.539
deepblue_extract_ids	0.002	0.001	0.002
deepblue_extract_names	0.001	0.000	0.001
deepblue_faceting_experiments	0.041	0.002	0.549
deepblue_filter_regions	0.031	0.001	0.274
deepblue_find_motif	0.035	0.001	0.279
deepblue_flank	0.055	0.002	0.537
deepblue_get_biosource_children	0.037	0.016	0.269
deepblue_get_biosource_parents	0.442	0.591	0.256
deepblue_get_biosource_related	0.034	0.014	0.274
deepblue_get_biosource_synonyms	0.427	0.471	0.265
deepblue_get_experiments_by_query	0.447	0.574	0.260
deepblue_get_regions	0.032	0.002	0.575
deepblue_get_request_data	0.089	0.003	1.541
deepblue_info	0.078	0.042	0.293
deepblue_input_regions	0.421	0.665	0.268
deepblue_intersection	0.053	0.002	0.775
deepblue_is_biosource	0.020	0.001	0.264
deepblue_liftover	0.561	0.052	3.109
deepblue_list_annotations	0.048	0.013	0.344
deepblue_list_biosources	0.344	0.334	0.262
deepblue_list_cached_requests	0.001	0.001	0.001
deepblue_list_column_types	0.099	0.027	0.434
deepblue_list_epigenetic_marks	0.958	0.484	1.146
deepblue_list_experiments	0.570	0.464	0.665
deepblue_list_expressions	0.552	0.494	0.516
deepblue_list_gene_models	0.423	0.473	0.266
deepblue_list_genes	0.723	0.515	1.054
deepblue_list_genomes	0.406	0.468	0.271
deepblue_list_in_use	1.016	0.493	1.852
deepblue_list_projects	0.432	0.510	0.266
deepblue_list_recent_experiments	0.419	0.442	0.279
deepblue_list_requests	0.015	0.001	0.257
deepblue_list_samples	0.281	0.126	0.708
deepblue_list_similar_biosources	0.120	0.095	0.433
deepblue_list_similar_epigenetic_marks	0.441	0.553	0.286
deepblue_list_similar_experiments	0.428	0.575	0.822
deepblue_list_similar_genomes	0.035	0.016	0.261
deepblue_list_similar_projects	0.461	0.764	0.264
deepblue_list_similar_techniques	0.456	0.620	0.263
deepblue_list_techniques	0.463	0.636	0.275
deepblue_merge_queries	0.471	0.595	0.788
deepblue_meta_data_to_table	0.764	0.813	0.750
deepblue_name_to_id	0.362	0.451	0.769
deepblue_overlap	0.080	0.003	0.806
deepblue_preview_experiment	0.022	0.001	0.268
deepblue_query_cache	0.095	0.004	1.059
deepblue_query_experiment_type	0.064	0.002	0.549
deepblue_reset_options	0.000	0.000	0.001
deepblue_score_matrix	0.058	0.002	0.860
deepblue_search	0.100	0.043	0.659
deepblue_select_annotations	0.445	0.723	0.272
deepblue_select_column	0.451	0.063	1.041
deepblue_select_experiments	0.418	0.686	0.264
deepblue_select_expressions	0.024	0.000	0.380
deepblue_select_genes	0.034	0.001	0.393
deepblue_select_regions	0.038	0.002	0.279
deepblue_tiling_regions	0.024	0.001	0.263