BioC 3.4: CHECK report for DeepBlueR on malbec1

Package: DeepBlueR

Version: 1.0.11

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DeepBlueR_1.0.11.tar.gz

StartedAt: 2017-04-14 22:00:34 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:04:31 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 236.8 seconds

RetCode: 0

Status:  OK

CheckDir: DeepBlueR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DeepBlueR_1.0.11.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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
* 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	0.096	0.004	1.646
deepblue_batch_export_results	0.388	0.000	4.579
deepblue_binning	0.056	0.000	1.615
deepblue_cache_status	0.004	0.000	0.004
deepblue_calculate_enrichment	0.084	0.000	1.901
deepblue_cancel_request	0.024	0.000	0.291
deepblue_chromosomes	0.080	0.000	0.322
deepblue_clear_cache	0.004	0.000	0.003
deepblue_collection_experiments_count	0.040	0.012	0.324
deepblue_commands	0.180	0.004	0.954
deepblue_count_gene_ontology_terms	0.108	0.000	0.662
deepblue_count_regions	0.048	0.004	1.638
deepblue_coverage	0.048	0.000	1.645
deepblue_delete_request_from_cache	0.004	0.000	0.005
deepblue_diff	0.140	0.008	0.663
deepblue_download_request_data	0.196	0.012	2.691
deepblue_echo	0.016	0.000	0.252
deepblue_export_bed	0.664	0.004	3.671
deepblue_export_meta_data	0.080	0.000	0.427
deepblue_export_tab	0.128	0.000	2.312
deepblue_extend	0.056	0.000	0.537
deepblue_extract_ids	0.004	0.000	0.002
deepblue_extract_names	0.004	0.000	0.001
deepblue_faceting_experiments	0.040	0.000	0.324
deepblue_filter_regions	0.032	0.004	0.291
deepblue_flank	0.064	0.000	0.546
deepblue_get_biosource_children	0.024	0.000	0.302
deepblue_get_biosource_parents	0.020	0.000	0.263
deepblue_get_biosource_related	0.024	0.000	0.283
deepblue_get_biosource_synonyms	0.020	0.000	0.264
deepblue_get_experiments_by_query	0.020	0.004	0.282
deepblue_get_regions	0.040	0.016	1.682
deepblue_get_request_data	0.088	0.004	2.213
deepblue_info	0.036	0.000	0.278
deepblue_input_regions	0.020	0.000	0.446
deepblue_intersection	0.060	0.008	1.707
deepblue_is_biosource	0.016	0.004	0.259
deepblue_liftover	0.440	0.004	3.127
deepblue_list_annotations	0.036	0.000	0.274
deepblue_list_biosources	0.024	0.000	0.293
deepblue_list_cached_requests	0.000	0.000	0.003
deepblue_list_column_types	0.080	0.000	0.424
deepblue_list_epigenetic_marks	0.440	0.004	1.000
deepblue_list_experiments	0.084	0.000	0.334
deepblue_list_expressions	0.224	0.004	0.677
deepblue_list_gene_models	0.020	0.000	0.289
deepblue_list_genes	0.428	0.004	1.315
deepblue_list_genomes	0.024	0.000	0.264
deepblue_list_in_use	0.240	0.000	1.307
deepblue_list_projects	0.024	0.000	0.294
deepblue_list_recent_experiments	0.088	0.000	0.328
deepblue_list_requests	0.020	0.000	0.258
deepblue_list_samples	0.128	0.004	0.703
deepblue_list_similar_biosources	0.036	0.000	0.537
deepblue_list_similar_epigenetic_marks	0.032	0.000	0.284
deepblue_list_similar_experiments	0.024	0.004	1.861
deepblue_list_similar_genomes	0.024	0.000	0.296
deepblue_list_similar_projects	0.024	0.000	0.266
deepblue_list_similar_techniques	0.028	0.000	0.268
deepblue_list_techniques	0.032	0.000	0.299
deepblue_merge_queries	0.080	0.000	1.579
deepblue_meta_data_to_table	0.132	0.000	0.720
deepblue_name_to_id	0.076	0.000	0.794
deepblue_overlap	0.112	0.008	1.579
deepblue_preview_experiment	0.024	0.000	0.271
deepblue_query_cache	0.112	0.004	1.819
deepblue_query_experiment_type	0.064	0.000	1.354
deepblue_reset_options	0.004	0.000	0.002
deepblue_score_matrix	0.112	0.004	0.617
deepblue_search	0.056	0.000	0.568
deepblue_select_annotations	0.032	0.000	0.276
deepblue_select_column	0.288	0.000	0.853
deepblue_select_experiments	0.032	0.000	1.008
deepblue_select_expressions	0.036	0.004	0.384
deepblue_select_genes	0.040	0.000	0.384
deepblue_select_regions	0.048	0.000	0.952
deepblue_tiling_regions	0.032	0.000	0.273