Package: DeepBlueR

Version: 1.4.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DeepBlueR_1.4.1.tar.gz

StartedAt: 2018-04-11 22:46:56 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:51:05 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 249.4 seconds

RetCode: 0

Status:  OK

CheckDir: DeepBlueR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DeepBlueR_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.1’
* 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 ... NOTE
prepare_Rd: deepblue_enrich_regions_fast.Rd:35-38: Dropping empty section \examples
* 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 1.456  0.028   5.586
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.

* 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	0.760	0.020	1.678
deepblue_batch_export_results	1.456	0.028	5.586
deepblue_binning	0.052	0.000	0.919
deepblue_cache_status	0.000	0.000	0.003
deepblue_cancel_request	0.016	0.000	0.284
deepblue_chromosomes	0.076	0.000	0.320
deepblue_clear_cache	0.000	0.000	0.002
deepblue_collection_experiments_count	0.100	0.004	0.597
deepblue_commands	0.148	0.000	0.928
deepblue_count_gene_ontology_terms	0.388	0.000	0.922
deepblue_count_regions	0.036	0.000	0.561
deepblue_coverage	0.040	0.000	0.872
deepblue_delete_request_from_cache	0.004	0.000	0.003
deepblue_diff	0.432	0.004	1.043
deepblue_distinct_column_values	0.04	0.00	1.13
deepblue_download_request_data	1.100	0.004	3.007
deepblue_echo	0.008	0.000	0.238
deepblue_enrich_regions_go_terms	0.072	0.000	1.093
deepblue_enrich_regions_overlap	0.756	0.044	4.496
deepblue_export_bed	0.364	0.000	2.901
deepblue_export_meta_data	0.276	0.000	0.662
deepblue_export_tab	0.12	0.00	1.65
deepblue_extend	0.040	0.000	0.501
deepblue_extract_ids	0.000	0.000	0.001
deepblue_extract_names	0.000	0.000	0.001
deepblue_faceting_experiments	0.040	0.000	0.671
deepblue_filter_regions	0.028	0.004	0.351
deepblue_find_motif	0.028	0.000	0.257
deepblue_flank	0.052	0.000	0.525
deepblue_get_biosource_children	0.024	0.000	0.263
deepblue_get_biosource_parents	0.016	0.000	0.289
deepblue_get_biosource_related	0.020	0.000	0.268
deepblue_get_biosource_synonyms	0.020	0.000	0.254
deepblue_get_experiments_by_query	0.052	0.004	0.301
deepblue_get_regions	0.044	0.000	0.994
deepblue_get_request_data	0.116	0.000	1.429
deepblue_info	0.040	0.000	0.311
deepblue_input_regions	0.020	0.004	0.505
deepblue_intersection	0.068	0.004	0.934
deepblue_is_biosource	0.016	0.000	0.240
deepblue_liftover	1.036	0.016	4.637
deepblue_list_annotations	0.020	0.004	0.255
deepblue_list_biosources	0.020	0.000	0.293
deepblue_list_cached_requests	0.000	0.004	0.004
deepblue_list_column_types	0.100	0.004	0.422
deepblue_list_epigenetic_marks	0.500	0.000	1.243
deepblue_list_experiments	0.232	0.000	0.699
deepblue_list_expressions	0.184	0.000	0.648
deepblue_list_gene_models	0.020	0.000	0.233
deepblue_list_genes	0.232	0.000	1.081
deepblue_list_genomes	0.02	0.00	0.26
deepblue_list_in_use	0.360	0.000	1.624
deepblue_list_projects	0.020	0.000	0.258
deepblue_list_recent_experiments	0.024	0.000	0.256
deepblue_list_requests	0.016	0.000	0.246
deepblue_list_samples	0.164	0.000	0.778
deepblue_list_similar_biosources	0.028	0.000	0.436
deepblue_list_similar_epigenetic_marks	0.028	0.000	0.277
deepblue_list_similar_experiments	0.016	0.000	0.910
deepblue_list_similar_genomes	0.020	0.000	0.277
deepblue_list_similar_projects	0.020	0.000	0.285
deepblue_list_similar_techniques	0.016	0.000	0.257
deepblue_list_techniques	0.028	0.000	0.290
deepblue_merge_queries	0.076	0.004	0.892
deepblue_meta_data_to_table	0.192	0.004	0.806
deepblue_name_to_id	0.072	0.000	0.729
deepblue_overlap	0.060	0.004	0.786
deepblue_preview_experiment	0.020	0.000	0.237
deepblue_query_cache	0.112	0.004	1.086
deepblue_query_experiment_type	0.060	0.000	1.501
deepblue_reset_options	0.004	0.000	0.001
deepblue_score_matrix	0.108	0.000	0.873
deepblue_search	0.060	0.000	0.587
deepblue_select_annotations	0.032	0.000	0.267
deepblue_select_column	0.552	0.000	1.310
deepblue_select_experiments	0.024	0.000	0.296
deepblue_select_expressions	0.056	0.000	0.406
deepblue_select_genes	0.032	0.000	0.372
deepblue_select_regions	0.076	0.000	1.243
deepblue_tiling_regions	0.028	0.000	0.236