Package: DeepBlueR

Version: 1.12.0

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_1.12.0.tar.gz

StartedAt: 2020-04-15 01:41:35 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:46:36 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 300.8 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.0’
* 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-3.10-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	0.082	0.010	0.772
deepblue_batch_export_results	0.365	0.034	3.741
deepblue_binning	0.052	0.002	0.507
deepblue_cache_status	0.003	0.001	0.004
deepblue_cancel_request	0.019	0.001	0.247
deepblue_chromosomes	0.073	0.003	0.298
deepblue_clear_cache	0.001	0.000	0.002
deepblue_collection_experiments_count	0.131	0.017	0.641
deepblue_commands	0.536	0.952	0.675
deepblue_count_gene_ontology_terms	0.125	0.031	0.573
deepblue_count_regions	0.466	0.927	0.486
deepblue_coverage	0.034	0.003	0.482
deepblue_delete_request_from_cache	0.002	0.001	0.003
deepblue_diff	0.131	0.029	0.612
deepblue_distinct_column_values	0.034	0.005	0.490
deepblue_download_request_data	0.231	0.021	2.020
deepblue_echo	0.017	0.001	0.247
deepblue_enrich_regions_go_terms	0.063	0.003	0.739
deepblue_enrich_regions_overlap	0.741	0.010	4.074
deepblue_export_bed	0.310	0.026	2.267
deepblue_export_meta_data	0.090	0.001	0.422
deepblue_export_tab	0.124	0.005	1.028
deepblue_extend	0.052	0.001	0.504
deepblue_extract_ids	0.001	0.000	0.001
deepblue_extract_names	0.001	0.000	0.002
deepblue_faceting_experiments	0.040	0.002	0.527
deepblue_filter_regions	0.030	0.001	0.255
deepblue_find_motif	0.031	0.001	0.261
deepblue_flank	0.053	0.002	0.504
deepblue_get_biosource_children	0.023	0.001	0.251
deepblue_get_biosource_parents	0.018	0.001	0.242
deepblue_get_biosource_related	0.022	0.001	0.254
deepblue_get_biosource_synonyms	0.015	0.001	0.239
deepblue_get_experiments_by_query	0.019	0.001	0.244
deepblue_get_regions	0.048	0.001	0.498
deepblue_get_request_data	0.094	0.003	1.255
deepblue_info	0.041	0.003	0.528
deepblue_input_regions	0.022	0.001	0.255
deepblue_intersection	0.075	0.002	0.751
deepblue_is_biosource	0.019	0.001	0.246
deepblue_liftover	1.114	0.040	4.069
deepblue_list_annotations	0.021	0.001	0.251
deepblue_list_biosources	0.020	0.001	0.250
deepblue_list_cached_requests	0.003	0.000	0.003
deepblue_list_column_types	0.071	0.008	0.398
deepblue_list_epigenetic_marks	0.805	0.724	0.966
deepblue_list_experiments	0.545	0.859	0.683
deepblue_list_expressions	1.319	0.523	0.494
deepblue_list_gene_models	0.402	0.896	0.241
deepblue_list_genes	0.304	0.065	1.003
deepblue_list_genomes	0.415	0.875	0.246
deepblue_list_in_use	0.516	0.023	1.592
deepblue_list_projects	0.425	0.715	0.242
deepblue_list_recent_experiments	0.023	0.001	0.253
deepblue_list_requests	0.012	0.001	0.237
deepblue_list_samples	0.178	0.011	0.659
deepblue_list_similar_biosources	0.029	0.001	0.428
deepblue_list_similar_epigenetic_marks	0.022	0.001	0.260
deepblue_list_similar_experiments	0.017	0.001	0.827
deepblue_list_similar_genomes	0.017	0.001	0.238
deepblue_list_similar_projects	0.021	0.001	0.245
deepblue_list_similar_techniques	0.019	0.000	0.245
deepblue_list_techniques	0.036	0.001	0.264
deepblue_merge_queries	0.077	0.002	0.747
deepblue_meta_data_to_table	0.146	0.004	0.712
deepblue_name_to_id	0.063	0.002	0.737
deepblue_overlap	0.083	0.002	0.763
deepblue_preview_experiment	0.016	0.000	0.244
deepblue_query_cache	0.090	0.003	0.991
deepblue_query_experiment_type	0.052	0.002	0.507
deepblue_reset_options	0.001	0.000	0.000
deepblue_score_matrix	0.039	0.002	0.495
deepblue_search	0.065	0.002	0.646
deepblue_select_annotations	0.032	0.001	0.256
deepblue_select_column	0.556	0.040	1.120
deepblue_select_experiments	0.611	0.630	0.248
deepblue_select_expressions	0.021	0.000	0.360
deepblue_select_genes	0.020	0.000	0.351
deepblue_select_regions	0.026	0.000	0.253
deepblue_tiling_regions	0.019	0.000	0.243