BioC 3.4: CHECK report for DeepBlueR on morelia

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: 2017-04-15 00:54:57 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:00:03 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 305.4 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_1.0.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 0.372  0.022   5.751
* 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	0.087	0.002	1.943
deepblue_batch_export_results	0.372	0.022	5.751
deepblue_binning	0.055	0.002	1.855
deepblue_cache_status	0.004	0.001	0.034
deepblue_calculate_enrichment	0.076	0.002	2.267
deepblue_cancel_request	0.014	0.000	0.371
deepblue_chromosomes	0.060	0.002	0.422
deepblue_clear_cache	0.002	0.001	0.618
deepblue_collection_experiments_count	0.053	0.002	0.443
deepblue_commands	0.157	0.008	1.247
deepblue_count_gene_ontology_terms	0.117	0.002	0.833
deepblue_count_regions	0.055	0.004	1.868
deepblue_coverage	0.069	0.006	1.891
deepblue_delete_request_from_cache	0.004	0.001	0.035
deepblue_diff	0.163	0.031	1.835
deepblue_download_request_data	0.176	0.011	3.248
deepblue_echo	0.013	0.000	0.369
deepblue_export_bed	0.557	0.011	4.622
deepblue_export_meta_data	0.084	0.002	0.653
deepblue_export_tab	0.125	0.004	2.753
deepblue_extend	0.070	0.002	0.791
deepblue_extract_ids	0.002	0.000	0.002
deepblue_extract_names	0.001	0.000	0.001
deepblue_faceting_experiments	0.031	0.001	0.427
deepblue_filter_regions	0.025	0.001	0.404
deepblue_flank	0.054	0.001	0.770
deepblue_get_biosource_children	0.023	0.000	0.386
deepblue_get_biosource_parents	0.021	0.000	0.379
deepblue_get_biosource_related	0.023	0.001	0.396
deepblue_get_biosource_synonyms	0.017	0.001	0.376
deepblue_get_experiments_by_query	0.018	0.002	0.394
deepblue_get_regions	0.054	0.006	1.898
deepblue_get_request_data	0.095	0.008	2.709
deepblue_info	0.034	0.004	0.403
deepblue_input_regions	0.018	0.003	0.544
deepblue_intersection	0.068	0.008	2.125
deepblue_is_biosource	0.018	0.002	0.378
deepblue_liftover	0.380	0.024	2.807
deepblue_list_annotations	0.032	0.001	0.391
deepblue_list_biosources	0.017	0.001	0.374
deepblue_list_cached_requests	0.003	0.001	0.036
deepblue_list_column_types	0.054	0.001	0.590
deepblue_list_epigenetic_marks	0.333	0.003	1.234
deepblue_list_experiments	0.103	0.002	0.472
deepblue_list_expressions	0.211	0.007	0.933
deepblue_list_gene_models	0.020	0.001	0.376
deepblue_list_genes	0.304	0.003	1.585
deepblue_list_genomes	0.020	0.001	0.376
deepblue_list_in_use	0.256	0.003	1.664
deepblue_list_projects	0.029	0.001	0.387
deepblue_list_recent_experiments	0.055	0.001	0.413
deepblue_list_requests	0.036	0.001	0.393
deepblue_list_samples	0.129	0.004	0.866
deepblue_list_similar_biosources	0.038	0.001	0.678
deepblue_list_similar_epigenetic_marks	0.027	0.000	0.395
deepblue_list_similar_experiments	0.015	0.000	1.933
deepblue_list_similar_genomes	0.018	0.001	0.375
deepblue_list_similar_projects	0.020	0.001	0.376
deepblue_list_similar_techniques	0.026	0.000	0.384
deepblue_list_techniques	0.028	0.000	0.388
deepblue_merge_queries	0.087	0.001	1.888
deepblue_meta_data_to_table	0.111	0.002	1.007
deepblue_name_to_id	0.074	0.002	1.146
deepblue_overlap	0.078	0.002	1.876
deepblue_preview_experiment	0.021	0.001	0.389
deepblue_query_cache	0.143	0.003	2.314
deepblue_query_experiment_type	0.086	0.002	1.579
deepblue_reset_options	0.001	0.000	0.000
deepblue_score_matrix	0.077	0.002	0.815
deepblue_search	0.103	0.004	0.735
deepblue_select_annotations	0.032	0.001	0.392
deepblue_select_column	0.199	0.001	1.104
deepblue_select_experiments	0.032	0.001	1.123
deepblue_select_expressions	0.038	0.001	0.575
deepblue_select_genes	0.032	0.001	0.566
deepblue_select_regions	0.038	0.000	1.075
deepblue_tiling_regions	0.026	0.000	0.384