BioC 3.5: CHECK report for DeepBlueR on oaxaca

Package: DeepBlueR

Version: 1.1.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DeepBlueR_1.1.9.tar.gz

StartedAt: 2017-03-04 01:38:29 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 01:43:45 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 316.7 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_1.1.9.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 r72177)
* 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 ‘1.1.9’
* 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 2.142  0.056   6.797
* 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	0.778	0.011	3.475
deepblue_batch_export_results	2.142	0.056	6.797
deepblue_binning	0.053	0.001	1.699
deepblue_cache_status	0.004	0.001	0.011
deepblue_cancel_request	0.019	0.001	0.375
deepblue_chromosomes	0.063	0.002	0.436
deepblue_clear_cache	0.002	0.000	0.003
deepblue_collection_experiments_count	0.036	0.000	0.423
deepblue_commands	0.138	0.006	1.253
deepblue_count_regions	0.040	0.001	1.321
deepblue_coverage	0.052	0.002	1.339
deepblue_delete_request_from_cache	0.003	0.001	0.004
deepblue_diff	0.401	0.014	1.214
deepblue_download_request_data	1.000	0.012	3.381
deepblue_echo	0.015	0.000	0.370
deepblue_export_bed	0.322	0.011	4.618
deepblue_export_meta_data	0.281	0.001	0.826
deepblue_export_tab	0.116	0.003	3.162
deepblue_extend	0.056	0.002	1.798
deepblue_extract_ids	0.001	0.000	0.002
deepblue_extract_names	0.001	0.000	0.001
deepblue_faceting_experiments	0.034	0.000	0.429
deepblue_filter_regions	0.027	0.001	0.894
deepblue_flank	0.055	0.002	1.826
deepblue_get_biosource_children	0.019	0.001	0.382
deepblue_get_biosource_parents	0.038	0.001	0.396
deepblue_get_biosource_related	0.023	0.000	0.395
deepblue_get_biosource_synonyms	0.021	0.001	0.380
deepblue_get_experiments_by_query	0.058	0.001	0.432
deepblue_get_regions	0.041	0.001	1.329
deepblue_get_request_data	0.118	0.002	2.113
deepblue_info	0.028	0.002	0.393
deepblue_input_regions	0.019	0.001	0.903
deepblue_intersection	0.062	0.002	2.768
deepblue_is_biosource	0.015	0.001	0.371
deepblue_liftover	0.629	0.016	3.978
deepblue_list_annotations	0.030	0.000	0.388
deepblue_list_biosources	0.019	0.000	0.375
deepblue_list_cached_requests	0.001	0.001	0.002
deepblue_list_column_types	0.085	0.001	0.628
deepblue_list_epigenetic_marks	0.485	0.008	1.422
deepblue_list_experiments	0.052	0.001	0.424
deepblue_list_expressions	0.103	0.001	0.653
deepblue_list_gene_models	0.013	0.000	0.367
deepblue_list_genes	0.350	0.004	1.664
deepblue_list_genomes	0.018	0.000	0.376
deepblue_list_in_use	0.213	0.001	1.804
deepblue_list_projects	0.018	0.000	0.374
deepblue_list_recent_experiments	0.036	0.001	0.392
deepblue_list_requests	0.017	0.001	0.373
deepblue_list_samples	0.097	0.004	0.866
deepblue_list_similar_biosources	0.027	0.001	1.426
deepblue_list_similar_epigenetic_marks	0.028	0.001	0.420
deepblue_list_similar_experiments	0.021	0.001	4.575
deepblue_list_similar_genomes	0.020	0.000	0.376
deepblue_list_similar_projects	0.016	0.000	0.372
deepblue_list_similar_techniques	0.013	0.001	0.371
deepblue_list_techniques	0.037	0.001	0.395
deepblue_merge_queries	0.048	0.002	2.732
deepblue_meta_data_to_table	0.284	0.003	1.190
deepblue_name_to_id	0.075	0.002	1.140
deepblue_overlap	0.073	0.002	2.769
deepblue_preview_experiment	0.018	0.000	0.393
deepblue_query_cache	0.145	0.003	3.706
deepblue_query_experiment_type	0.046	0.001	1.280
deepblue_reset_options	0.001	0.000	0.001
deepblue_score_matrix	0.045	0.002	1.298
deepblue_search	0.039	0.001	0.657
deepblue_select_annotations	0.030	0.001	0.905
deepblue_select_column	0.276	0.002	1.204
deepblue_select_experiments	0.025	0.000	0.960
deepblue_select_expressions	0.035	0.001	1.091
deepblue_select_genes	0.028	0.000	1.077
deepblue_select_regions	0.087	0.001	0.979
deepblue_tiling_regions	0.068	0.001	0.942