BioC 3.4: CHECK report for DeepBlueR on morelia

Package: DeepBlueR

Version: 0.99.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DeepBlueR_0.99.2.tar.gz

StartedAt: 2016-09-20 05:26:54 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:29:11 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 137.4 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_0.99.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘0.99.2’
* 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	0.073	0.002	1.483
deepblue_batch_export_results	0.179	0.006	2.536
deepblue_cancel_request	0.017	0.000	0.387
deepblue_chromosomes	0.097	0.003	0.449
deepblue_collection_experiments_count	0.053	0.001	0.417
deepblue_commands	1.116	0.020	2.582
deepblue_count_regions	0.032	0.001	0.925
deepblue_coverage	0.051	0.001	0.966
deepblue_download_request_data	0.112	0.004	2.071
deepblue_echo	0.014	0.001	0.355
deepblue_extend	0.059	0.001	0.988
deepblue_extract_ids	0.001	0.000	0.001
deepblue_extract_names	0.001	0.000	0.001
deepblue_faceting_experiments	0.115	0.002	0.482
deepblue_filter_regions	0.031	0.001	0.518
deepblue_flank	0.045	0.001	0.977
deepblue_get_biosource_children	0.026	0.000	0.373
deepblue_get_biosource_parents	0.017	0.000	0.366
deepblue_get_biosource_related	0.024	0.001	0.377
deepblue_get_biosource_synonyms	0.024	0.001	0.392
deepblue_get_experiments_by_query	0.019	0.001	0.383
deepblue_get_regions	0.046	0.001	0.890
deepblue_get_request_data	0.088	0.002	1.749
deepblue_info	0.097	0.002	0.442
deepblue_input_regions	0.024	0.001	0.485
deepblue_intersection	0.065	0.002	1.485
deepblue_is_biosource	0.017	0.001	0.358
deepblue_list_annotations	0.044	0.001	0.413
deepblue_list_biosources	0.024	0.000	0.372
deepblue_list_column_types	0.127	0.002	0.638
deepblue_list_epigenetic_marks	1.009	0.019	1.900
deepblue_list_experiments	0.121	0.002	0.481
deepblue_list_gene_expressions	0.027	0.001	0.377
deepblue_list_gene_models	0.016	0.000	0.383
deepblue_list_genes	0.141	0.004	0.941
deepblue_list_genomes	0.020	0.001	0.368
deepblue_list_in_use	0.559	0.010	2.035
deepblue_list_projects	0.019	0.000	0.387
deepblue_list_recent_experiments	0.038	0.000	0.380
deepblue_list_requests	0.018	0.001	0.595
deepblue_list_samples	0.161	0.003	0.911
deepblue_list_similar_biosources	0.048	0.001	0.560
deepblue_list_similar_epigenetic_marks	0.040	0.001	0.415
deepblue_list_similar_experiments	0.02	0.00	2.39
deepblue_list_similar_genomes	0.020	0.000	0.361
deepblue_list_similar_projects	0.019	0.000	0.366
deepblue_list_similar_techniques	0.022	0.001	0.365
deepblue_list_techniques	0.044	0.001	0.392
deepblue_merge_queries	0.070	0.002	1.569
deepblue_name_to_id	0.063	0.002	1.107
deepblue_preview_experiment	0.013	0.000	0.362
deepblue_query_cache	0.078	0.003	1.897
deepblue_query_experiment_type	0.050	0.001	0.879
deepblue_score_matrix	0.053	0.001	0.879
deepblue_search	0.074	0.002	0.632
deepblue_select_annotations	0.021	0.001	0.506
deepblue_select_experiments	0.019	0.000	0.492
deepblue_select_gene_expressions	0.021	0.000	0.663
deepblue_select_genes	0.032	0.001	0.665
deepblue_select_regions	0.040	0.001	0.503
deepblue_tiling_regions	0.029	0.001	0.492