Package: DeepBlueR

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DeepBlueR_1.4.1.tar.gz

StartedAt: 2018-04-12 02:37:13 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:41:46 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 272.6 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 --no-vignettes --timings DeepBlueR_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.1’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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-3.6-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.

* installing *source* package ‘DeepBlueR’ ...
** R
** demo
** inst
** preparing 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	0.941	0.034	1.879
deepblue_batch_export_results	1.374	0.018	4.974
deepblue_binning	0.033	0.001	0.973
deepblue_cache_status	0.002	0.001	0.003
deepblue_cancel_request	0.014	0.001	0.255
deepblue_chromosomes	0.069	0.002	0.314
deepblue_clear_cache	0.002	0.000	0.003
deepblue_collection_experiments_count	0.122	0.001	0.633
deepblue_commands	0.124	0.007	0.947
deepblue_count_gene_ontology_terms	0.289	0.002	0.878
deepblue_count_regions	0.029	0.001	0.491
deepblue_coverage	0.034	0.002	0.865
deepblue_delete_request_from_cache	0.002	0.001	0.003
deepblue_diff	0.384	0.014	0.871
deepblue_distinct_column_values	0.036	0.002	0.887
deepblue_download_request_data	0.785	0.009	2.731
deepblue_echo	0.013	0.001	0.249
deepblue_enrich_regions_go_terms	0.060	0.002	1.206
deepblue_enrich_regions_overlap	0.677	0.007	4.744
deepblue_export_bed	0.268	0.008	2.840
deepblue_export_meta_data	0.267	0.002	0.625
deepblue_export_tab	0.098	0.003	1.643
deepblue_extend	0.040	0.002	0.515
deepblue_extract_ids	0.001	0.000	0.001
deepblue_extract_names	0.001	0.000	0.001
deepblue_faceting_experiments	0.030	0.001	0.739
deepblue_filter_regions	0.025	0.000	0.312
deepblue_find_motif	0.022	0.001	0.252
deepblue_flank	0.041	0.001	0.514
deepblue_get_biosource_children	0.017	0.000	0.251
deepblue_get_biosource_parents	0.012	0.000	0.242
deepblue_get_biosource_related	0.018	0.001	0.255
deepblue_get_biosource_synonyms	0.014	0.001	0.250
deepblue_get_experiments_by_query	0.042	0.001	0.293
deepblue_get_regions	0.029	0.001	1.314
deepblue_get_request_data	0.101	0.003	1.470
deepblue_info	0.034	0.001	0.265
deepblue_input_regions	0.019	0.000	0.518
deepblue_intersection	0.050	0.002	0.997
deepblue_is_biosource	0.014	0.001	0.250
deepblue_liftover	1.025	0.063	4.201
deepblue_list_annotations	0.026	0.001	0.254
deepblue_list_biosources	0.018	0.001	0.254
deepblue_list_cached_requests	0.002	0.000	0.014
deepblue_list_column_types	0.082	0.001	0.441
deepblue_list_epigenetic_marks	0.496	0.022	1.209
deepblue_list_experiments	0.157	0.001	0.635
deepblue_list_expressions	0.133	0.001	0.590
deepblue_list_gene_models	0.016	0.001	0.246
deepblue_list_genes	0.279	0.005	1.085
deepblue_list_genomes	0.011	0.000	0.247
deepblue_list_in_use	0.411	0.005	1.618
deepblue_list_projects	0.018	0.001	0.248
deepblue_list_recent_experiments	0.026	0.001	0.261
deepblue_list_requests	0.016	0.001	0.247
deepblue_list_samples	0.182	0.011	0.807
deepblue_list_similar_biosources	0.028	0.001	0.442
deepblue_list_similar_epigenetic_marks	0.025	0.001	0.273
deepblue_list_similar_experiments	0.016	0.000	0.840
deepblue_list_similar_genomes	0.018	0.000	0.258
deepblue_list_similar_projects	0.017	0.000	0.258
deepblue_list_similar_techniques	0.015	0.001	0.251
deepblue_list_techniques	0.027	0.001	0.258
deepblue_merge_queries	0.058	0.001	0.777
deepblue_meta_data_to_table	0.255	0.004	0.852
deepblue_name_to_id	0.086	0.002	0.790
deepblue_overlap	0.117	0.005	0.828
deepblue_preview_experiment	0.017	0.000	0.298
deepblue_query_cache	0.110	0.002	1.059
deepblue_query_experiment_type	0.047	0.002	1.581
deepblue_reset_options	0.000	0.000	0.001
deepblue_score_matrix	0.076	0.002	0.945
deepblue_search	0.052	0.001	0.611
deepblue_select_annotations	0.024	0.001	0.262
deepblue_select_column	0.450	0.010	1.226
deepblue_select_experiments	0.020	0.001	0.261
deepblue_select_expressions	0.028	0.001	0.378
deepblue_select_genes	0.024	0.001	0.380
deepblue_select_regions	0.065	0.001	1.237
deepblue_tiling_regions	0.019	0.001	0.267