Package: DeepBlueR

Version: 1.10.0

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_1.10.0.tar.gz

StartedAt: 2019-10-16 02:03:33 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:09:36 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 362.5 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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.0’
* 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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DeepBlueR)

name	user	system	elapsed
deepblue_aggregate	0.113	0.017	0.727
deepblue_batch_export_results	0.529	0.066	3.360
deepblue_binning	0.063	0.003	0.464
deepblue_cache_status	0.003	0.001	0.005
deepblue_cancel_request	0.023	0.001	0.222
deepblue_chromosomes	0.071	0.004	0.328
deepblue_clear_cache	0.002	0.001	0.003
deepblue_collection_experiments_count	0.152	0.014	0.522
deepblue_commands	0.667	0.560	0.690
deepblue_count_gene_ontology_terms	0.225	0.031	0.616
deepblue_count_regions	0.508	0.540	0.463
deepblue_coverage	0.051	0.005	0.459
deepblue_delete_request_from_cache	0.003	0.002	0.006
deepblue_diff	0.207	0.059	0.669
deepblue_distinct_column_values	0.068	0.012	0.483
deepblue_download_request_data	0.348	0.043	2.049
deepblue_echo	0.020	0.002	0.221
deepblue_enrich_regions_go_terms	0.097	0.004	0.755
deepblue_enrich_regions_overlap	0.872	0.033	4.114
deepblue_export_bed	1.084	0.051	3.244
deepblue_export_meta_data	0.076	0.003	0.378
deepblue_export_tab	0.154	0.011	0.969
deepblue_extend	0.065	0.002	0.468
deepblue_extract_ids	0.001	0.000	0.001
deepblue_extract_names	0.001	0.001	0.001
deepblue_faceting_experiments	0.042	0.002	0.498
deepblue_filter_regions	0.038	0.001	0.248
deepblue_find_motif	0.043	0.001	0.239
deepblue_flank	0.055	0.002	0.449
deepblue_get_biosource_children	0.025	0.001	0.225
deepblue_get_biosource_parents	0.023	0.001	0.222
deepblue_get_biosource_related	0.025	0.002	0.229
deepblue_get_biosource_synonyms	0.023	0.001	0.222
deepblue_get_experiments_by_query	0.014	0.001	0.214
deepblue_get_regions	0.056	0.003	0.452
deepblue_get_request_data	0.113	0.005	1.410
deepblue_info	0.059	0.005	0.262
deepblue_input_regions	0.026	0.002	0.515
deepblue_intersection	0.087	0.004	1.006
deepblue_is_biosource	0.021	0.001	0.219
deepblue_liftover	0.621	0.100	3.896
deepblue_list_annotations	0.038	0.002	0.239
deepblue_list_biosources	0.026	0.002	0.225
deepblue_list_cached_requests	0.003	0.002	0.004
deepblue_list_column_types	0.081	0.011	0.369
deepblue_list_epigenetic_marks	1.056	0.460	1.153
deepblue_list_experiments	1.198	0.196	0.669
deepblue_list_expressions	0.673	0.501	0.630
deepblue_list_gene_models	0.418	0.453	0.230
deepblue_list_genes	0.599	0.099	1.253
deepblue_list_genomes	0.337	0.322	0.233
deepblue_list_in_use	0.653	0.034	1.631
deepblue_list_projects	0.407	0.466	0.228
deepblue_list_recent_experiments	0.041	0.001	0.247
deepblue_list_requests	0.029	0.001	0.231
deepblue_list_samples	0.263	0.029	0.694
deepblue_list_similar_biosources	0.042	0.002	0.336
deepblue_list_similar_epigenetic_marks	0.038	0.001	0.243
deepblue_list_similar_experiments	0.027	0.002	0.781
deepblue_list_similar_genomes	0.021	0.002	0.219
deepblue_list_similar_projects	0.019	0.002	0.220
deepblue_list_similar_techniques	0.031	0.002	0.229
deepblue_list_techniques	0.047	0.003	0.248
deepblue_merge_queries	0.090	0.004	0.687
deepblue_meta_data_to_table	0.169	0.008	0.667
deepblue_name_to_id	0.075	0.004	0.741
deepblue_overlap	0.104	0.004	0.706
deepblue_preview_experiment	0.025	0.001	0.229
deepblue_query_cache	0.116	0.005	1.532
deepblue_query_experiment_type	0.077	0.002	1.007
deepblue_reset_options	0.001	0.000	0.000
deepblue_score_matrix	0.063	0.003	0.478
deepblue_search	0.077	0.007	0.854
deepblue_select_annotations	0.039	0.002	0.298
deepblue_select_column	0.768	0.032	1.414
deepblue_select_experiments	0.400	0.452	0.229
deepblue_select_expressions	0.038	0.002	0.334
deepblue_select_genes	0.042	0.001	0.336
deepblue_select_regions	0.051	0.001	0.253
deepblue_tiling_regions	0.032	0.001	0.233