BioC 3.5: CHECK report for DeepBlueR on veracruz2

Package: DeepBlueR

Version: 1.2.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DeepBlueR_1.2.10.tar.gz

StartedAt: 2017-08-16 01:50:36 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:55:11 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 275.5 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 --no-vignettes --timings DeepBlueR_1.2.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.2.10’
* 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 ... OK
* 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
Examples with CPU or elapsed time > 5s
                               user system elapsed
deepblue_batch_export_results 1.839  0.028   6.055
* 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: OK

* 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	0.631	0.009	1.376
deepblue_batch_export_results	1.839	0.028	6.055
deepblue_binning	0.045	0.006	0.891
deepblue_cache_status	0.003	0.000	0.003
deepblue_cancel_request	0.017	0.002	0.246
deepblue_chromosomes	0.070	0.011	0.327
deepblue_clear_cache	0.001	0.000	0.002
deepblue_collection_experiments_count	0.042	0.006	0.305
deepblue_commands	0.146	0.011	1.010
deepblue_count_gene_ontology_terms	0.127	0.002	0.710
deepblue_count_regions	0.034	0.001	0.864
deepblue_coverage	0.030	0.002	0.866
deepblue_delete_request_from_cache	0.003	0.001	0.004
deepblue_diff	0.258	0.011	0.745
deepblue_distinct_column_values	0.026	0.002	0.857
deepblue_download_request_data	0.978	0.010	2.882
deepblue_echo	0.008	0.001	0.238
deepblue_enrich_region_overlap	0.658	0.012	4.625
deepblue_enrich_regions_go_terms	0.086	0.002	1.188
deepblue_export_bed	0.286	0.009	2.693
deepblue_export_meta_data	0.273	0.002	0.633
deepblue_export_tab	0.097	0.004	1.479
deepblue_extend	0.046	0.002	0.514
deepblue_extract_ids	0.001	0.000	0.002
deepblue_extract_names	0.002	0.000	0.002
deepblue_faceting_experiments	0.031	0.001	0.300
deepblue_filter_regions	0.022	0.001	0.278
deepblue_find_motif	0.026	0.001	0.256
deepblue_flank	0.037	0.001	0.499
deepblue_get_biosource_children	0.015	0.001	0.244
deepblue_get_biosource_parents	0.011	0.000	0.242
deepblue_get_biosource_related	0.020	0.001	0.260
deepblue_get_biosource_synonyms	0.014	0.001	0.243
deepblue_get_experiments_by_query	0.035	0.001	0.280
deepblue_get_regions	0.035	0.002	0.924
deepblue_get_request_data	0.104	0.002	1.453
deepblue_info	0.035	0.002	0.276
deepblue_input_regions	0.018	0.001	0.460
deepblue_intersection	0.054	0.002	0.971
deepblue_is_biosource	0.012	0.001	0.244
deepblue_liftover	0.586	0.036	4.701
deepblue_list_annotations	0.030	0.002	0.265
deepblue_list_biosources	0.017	0.000	0.246
deepblue_list_cached_requests	0.002	0.000	0.003
deepblue_list_column_types	0.287	0.002	0.640
deepblue_list_epigenetic_marks	0.302	0.001	0.931
deepblue_list_experiments	0.069	0.001	0.318
deepblue_list_expressions	0.168	0.001	0.643
deepblue_list_gene_models	0.016	0.000	0.246
deepblue_list_genes	0.286	0.004	1.176
deepblue_list_genomes	0.017	0.001	0.245
deepblue_list_in_use	0.298	0.002	1.398
deepblue_list_projects	0.018	0.000	0.247
deepblue_list_recent_experiments	0.027	0.001	0.258
deepblue_list_requests	0.016	0.001	0.246
deepblue_list_samples	0.107	0.004	0.619
deepblue_list_similar_biosources	0.029	0.001	1.038
deepblue_list_similar_epigenetic_marks	0.025	0.001	0.303
deepblue_list_similar_experiments	0.019	0.001	1.675
deepblue_list_similar_genomes	0.015	0.001	0.244
deepblue_list_similar_projects	0.018	0.001	0.257
deepblue_list_similar_techniques	0.017	0.001	0.252
deepblue_list_techniques	0.031	0.001	0.262
deepblue_merge_queries	0.065	0.002	0.776
deepblue_meta_data_to_table	0.311	0.003	1.208
deepblue_name_to_id	0.071	0.002	0.762
deepblue_overlap	0.065	0.002	0.762
deepblue_preview_experiment	0.016	0.000	0.276
deepblue_query_cache	0.108	0.003	1.035
deepblue_query_experiment_type	0.051	0.002	1.287
deepblue_reset_options	0.001	0.000	0.001
deepblue_score_matrix	0.088	0.002	0.941
deepblue_search	0.071	0.003	0.617
deepblue_select_annotations	0.027	0.000	0.262
deepblue_select_column	0.457	0.002	1.219
deepblue_select_experiments	0.018	0.001	0.250
deepblue_select_expressions	0.043	0.001	0.382
deepblue_select_genes	0.031	0.001	0.380
deepblue_select_regions	0.063	0.001	0.917
deepblue_tiling_regions	0.018	0.001	0.254