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: 2017-10-18 02:34:11 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:38:56 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 285.5 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 3.4.2 (2017-09-28)
* 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 1.767  0.019   5.324
* 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	0.612	0.007	1.379
deepblue_batch_export_results	1.767	0.019	5.324
deepblue_binning	0.033	0.001	0.884
deepblue_cache_status	0.002	0.000	0.003
deepblue_cancel_request	0.015	0.001	0.243
deepblue_chromosomes	0.043	0.001	0.289
deepblue_clear_cache	0.001	0.001	0.001
deepblue_collection_experiments_count	0.092	0.003	0.597
deepblue_commands	0.136	0.017	0.990
deepblue_count_gene_ontology_terms	0.229	0.020	0.830
deepblue_count_regions	0.024	0.002	0.869
deepblue_coverage	0.032	0.001	0.882
deepblue_delete_request_from_cache	0.003	0.001	0.004
deepblue_diff	0.363	0.016	0.857
deepblue_distinct_column_values	0.034	0.001	0.881
deepblue_download_request_data	1.151	0.012	3.076
deepblue_echo	0.009	0.000	0.241
deepblue_enrich_region_overlap	0.667	0.013	4.674
deepblue_enrich_regions_go_terms	0.084	0.002	1.212
deepblue_export_bed	0.260	0.011	2.688
deepblue_export_meta_data	0.200	0.002	0.560
deepblue_export_tab	0.092	0.003	1.499
deepblue_extend	0.038	0.001	0.688
deepblue_extract_ids	0.001	0.000	0.001
deepblue_extract_names	0.001	0.000	0.001
deepblue_faceting_experiments	0.021	0.001	1.387
deepblue_filter_regions	0.016	0.001	0.293
deepblue_find_motif	0.019	0.000	0.319
deepblue_flank	0.031	0.001	0.492
deepblue_get_biosource_children	0.014	0.001	0.517
deepblue_get_biosource_parents	0.016	0.000	0.249
deepblue_get_biosource_related	0.014	0.000	0.257
deepblue_get_biosource_synonyms	0.019	0.000	0.251
deepblue_get_experiments_by_query	0.034	0.000	0.283
deepblue_get_regions	0.027	0.001	0.929
deepblue_get_request_data	0.100	0.003	1.465
deepblue_info	0.027	0.002	0.269
deepblue_input_regions	0.014	0.000	0.554
deepblue_intersection	0.056	0.001	1.051
deepblue_is_biosource	0.014	0.001	0.241
deepblue_liftover	0.634	0.038	3.220
deepblue_list_annotations	0.027	0.001	0.259
deepblue_list_biosources	0.018	0.001	0.246
deepblue_list_cached_requests	0.002	0.000	0.003
deepblue_list_column_types	0.087	0.001	0.427
deepblue_list_epigenetic_marks	0.511	0.003	1.269
deepblue_list_experiments	0.190	0.001	0.701
deepblue_list_expressions	0.159	0.001	0.624
deepblue_list_gene_models	0.015	0.000	0.241
deepblue_list_genes	0.300	0.004	1.125
deepblue_list_genomes	0.015	0.001	0.242
deepblue_list_in_use	0.383	0.005	1.683
deepblue_list_projects	0.012	0.001	0.240
deepblue_list_recent_experiments	0.025	0.000	0.252
deepblue_list_requests	0.013	0.000	0.239
deepblue_list_samples	0.131	0.007	0.719
deepblue_list_similar_biosources	0.025	0.000	0.913
deepblue_list_similar_epigenetic_marks	0.018	0.001	0.316
deepblue_list_similar_experiments	0.018	0.001	2.542
deepblue_list_similar_genomes	0.014	0.001	0.242
deepblue_list_similar_projects	0.013	0.001	0.240
deepblue_list_similar_techniques	0.014	0.000	0.244
deepblue_list_techniques	0.027	0.001	0.258
deepblue_merge_queries	0.053	0.002	0.772
deepblue_meta_data_to_table	0.268	0.004	0.857
deepblue_name_to_id	0.086	0.002	0.776
deepblue_overlap	0.060	0.002	0.754
deepblue_preview_experiment	0.015	0.001	0.267
deepblue_query_cache	0.098	0.002	1.033
deepblue_query_experiment_type	0.048	0.002	1.739
deepblue_reset_options	0.001	0.000	0.001
deepblue_score_matrix	0.071	0.001	1.003
deepblue_search	0.044	0.002	0.606
deepblue_select_annotations	0.022	0.001	0.256
deepblue_select_column	0.444	0.003	1.197
deepblue_select_experiments	0.019	0.001	0.254
deepblue_select_expressions	0.020	0.001	0.364
deepblue_select_genes	0.026	0.001	0.366
deepblue_select_regions	0.067	0.001	1.350
deepblue_tiling_regions	0.019	0.000	0.254