BioC 3.5: CHECK report for DeepBlueR on toluca2

Package: DeepBlueR

Version: 1.0.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DeepBlueR_1.0.11.tar.gz

StartedAt: 2017-04-23 02:46:48 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 02:51:58 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 310.3 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_1.0.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DeepBlueR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.11’
* 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 2.209  0.062   6.083
* 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	0.851	0.014	2.301
deepblue_batch_export_results	2.209	0.062	6.083
deepblue_binning	0.058	0.001	1.582
deepblue_cache_status	0.003	0.000	0.004
deepblue_calculate_enrichment	0.089	0.002	1.857
deepblue_cancel_request	0.024	0.001	0.248
deepblue_chromosomes	0.073	0.001	0.301
deepblue_clear_cache	0.002	0.000	0.002
deepblue_collection_experiments_count	0.038	0.001	0.619
deepblue_commands	0.145	0.006	0.947
deepblue_count_gene_ontology_terms	0.108	0.001	0.667
deepblue_count_regions	0.049	0.001	1.585
deepblue_coverage	0.057	0.001	1.598
deepblue_delete_request_from_cache	0.003	0.001	0.004
deepblue_diff	0.403	0.014	0.874
deepblue_download_request_data	0.979	0.010	3.260
deepblue_echo	0.013	0.001	0.235
deepblue_export_bed	0.338	0.009	3.185
deepblue_export_meta_data	0.256	0.003	0.594
deepblue_export_tab	0.111	0.003	2.178
deepblue_extend	0.055	0.002	0.504
deepblue_extract_ids	0.002	0.000	0.001
deepblue_extract_names	0.001	0.000	0.001
deepblue_faceting_experiments	0.033	0.001	0.293
deepblue_filter_regions	0.064	0.001	0.311
deepblue_flank	0.078	0.002	0.528
deepblue_get_biosource_children	0.020	0.001	0.249
deepblue_get_biosource_parents	0.015	0.000	0.238
deepblue_get_biosource_related	0.019	0.000	0.261
deepblue_get_biosource_synonyms	0.026	0.001	0.252
deepblue_get_experiments_by_query	0.058	0.001	0.297
deepblue_get_regions	0.044	0.001	1.637
deepblue_get_request_data	0.131	0.002	2.114
deepblue_info	0.031	0.002	0.261
deepblue_input_regions	0.020	0.000	0.405
deepblue_intersection	0.079	0.001	1.640
deepblue_is_biosource	0.023	0.001	0.246
deepblue_liftover	0.625	0.018	3.082
deepblue_list_annotations	0.028	0.001	0.252
deepblue_list_biosources	0.020	0.001	0.243
deepblue_list_cached_requests	0.002	0.000	0.003
deepblue_list_column_types	0.342	0.002	0.680
deepblue_list_epigenetic_marks	0.321	0.005	0.889
deepblue_list_experiments	0.065	0.001	0.299
deepblue_list_expressions	0.156	0.001	0.603
deepblue_list_gene_models	0.016	0.000	0.239
deepblue_list_genes	0.356	0.004	1.160
deepblue_list_genomes	0.017	0.000	0.240
deepblue_list_in_use	0.237	0.002	1.314
deepblue_list_projects	0.020	0.000	0.243
deepblue_list_recent_experiments	0.039	0.000	0.261
deepblue_list_requests	0.023	0.000	0.247
deepblue_list_samples	0.109	0.004	0.586
deepblue_list_similar_biosources	0.035	0.001	0.535
deepblue_list_similar_epigenetic_marks	0.027	0.000	0.261
deepblue_list_similar_experiments	0.021	0.000	1.796
deepblue_list_similar_genomes	0.024	0.001	0.251
deepblue_list_similar_projects	0.018	0.001	0.240
deepblue_list_similar_techniques	0.028	0.001	0.251
deepblue_list_techniques	0.049	0.001	0.273
deepblue_merge_queries	0.079	0.002	1.473
deepblue_meta_data_to_table	0.323	0.003	0.887
deepblue_name_to_id	0.109	0.002	0.777
deepblue_overlap	0.091	0.002	1.475
deepblue_preview_experiment	0.025	0.001	0.257
deepblue_query_cache	0.161	0.003	1.797
deepblue_query_experiment_type	0.063	0.001	1.264
deepblue_reset_options	0.001	0.000	0.001
deepblue_score_matrix	0.054	0.002	0.522
deepblue_search	0.053	0.001	0.548
deepblue_select_annotations	0.027	0.000	0.252
deepblue_select_column	0.256	0.001	0.825
deepblue_select_experiments	0.026	0.001	0.968
deepblue_select_expressions	0.030	0.001	0.363
deepblue_select_genes	0.028	0.001	0.360
deepblue_select_regions	0.098	0.001	0.987
deepblue_tiling_regions	0.065	0.000	0.289