BioC 3.6: CHECK report for DeepBlueR on veracruz1

Package: DeepBlueR

Version: 1.3.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DeepBlueR_1.3.10.tar.gz

StartedAt: 2017-08-16 02:04:37 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:09:07 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 270.4 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_1.3.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.3.10’
* 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
* 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	0.959	0.011	1.705
deepblue_batch_export_results	1.236	0.050	4.754
deepblue_binning	0.042	0.001	0.873
deepblue_cache_status	0.003	0.001	0.003
deepblue_cancel_request	0.013	0.001	0.242
deepblue_chromosomes	0.053	0.001	0.299
deepblue_clear_cache	0.001	0.000	0.002
deepblue_collection_experiments_count	0.030	0.001	0.295
deepblue_commands	0.150	0.007	1.001
deepblue_count_gene_ontology_terms	0.111	0.001	0.696
deepblue_count_regions	0.029	0.001	0.871
deepblue_coverage	0.030	0.001	0.856
deepblue_delete_request_from_cache	0.002	0.001	0.004
deepblue_diff	0.343	0.015	0.841
deepblue_distinct_column_values	0.036	0.001	0.879
deepblue_download_request_data	0.770	0.010	2.593
deepblue_echo	0.011	0.001	0.239
deepblue_enrich_region_overlap	0.716	0.007	4.607
deepblue_enrich_regions_go_terms	0.082	0.002	1.187
deepblue_export_bed	0.252	0.009	2.656
deepblue_export_meta_data	0.234	0.001	0.586
deepblue_export_tab	0.098	0.004	1.452
deepblue_extend	0.041	0.002	0.506
deepblue_extract_ids	0.001	0.000	0.001
deepblue_extract_names	0.001	0.000	0.002
deepblue_faceting_experiments	0.027	0.001	0.293
deepblue_filter_regions	0.026	0.001	0.285
deepblue_find_motif	0.027	0.001	0.258
deepblue_flank	0.059	0.002	0.520
deepblue_get_biosource_children	0.020	0.000	0.257
deepblue_get_biosource_parents	0.015	0.001	0.249
deepblue_get_biosource_related	0.019	0.001	0.265
deepblue_get_biosource_synonyms	0.017	0.001	0.247
deepblue_get_experiments_by_query	0.047	0.001	0.298
deepblue_get_regions	0.038	0.001	0.935
deepblue_get_request_data	0.100	0.003	1.442
deepblue_info	0.029	0.001	0.267
deepblue_input_regions	0.017	0.000	0.443
deepblue_intersection	0.061	0.001	0.976
deepblue_is_biosource	0.014	0.000	0.244
deepblue_liftover	0.617	0.044	3.349
deepblue_list_annotations	0.030	0.001	0.260
deepblue_list_biosources	0.014	0.001	0.242
deepblue_list_cached_requests	0.002	0.000	0.003
deepblue_list_column_types	0.301	0.005	0.658
deepblue_list_epigenetic_marks	0.299	0.002	0.925
deepblue_list_experiments	0.061	0.001	0.311
deepblue_list_expressions	0.177	0.001	0.653
deepblue_list_gene_models	0.017	0.001	0.246
deepblue_list_genes	0.283	0.004	1.167
deepblue_list_genomes	0.018	0.001	0.247
deepblue_list_in_use	0.317	0.002	1.353
deepblue_list_projects	0.017	0.001	0.251
deepblue_list_recent_experiments	0.030	0.001	0.266
deepblue_list_requests	0.016	0.001	0.245
deepblue_list_samples	0.096	0.003	0.593
deepblue_list_similar_biosources	0.021	0.001	0.999
deepblue_list_similar_epigenetic_marks	0.023	0.001	0.299
deepblue_list_similar_experiments	0.018	0.001	1.638
deepblue_list_similar_genomes	0.017	0.001	0.247
deepblue_list_similar_projects	0.017	0.001	0.252
deepblue_list_similar_techniques	0.019	0.001	0.251
deepblue_list_techniques	0.030	0.001	0.265
deepblue_merge_queries	0.060	0.002	0.757
deepblue_meta_data_to_table	0.304	0.004	0.901
deepblue_name_to_id	0.087	0.002	0.781
deepblue_overlap	0.065	0.002	0.767
deepblue_preview_experiment	0.016	0.000	0.269
deepblue_query_cache	0.109	0.003	1.053
deepblue_query_experiment_type	0.069	0.002	1.238
deepblue_reset_options	0.001	0.000	0.001
deepblue_score_matrix	0.074	0.002	0.972
deepblue_search	0.049	0.001	0.591
deepblue_select_annotations	0.026	0.000	0.257
deepblue_select_column	0.461	0.002	1.229
deepblue_select_experiments	0.021	0.001	0.252
deepblue_select_expressions	0.025	0.001	0.368
deepblue_select_genes	0.027	0.001	0.371
deepblue_select_regions	0.057	0.001	0.918
deepblue_tiling_regions	0.018	0.001	0.253