BioC 3.5: CHECK report for DeepBlueR on malbec2

Package: DeepBlueR

Version: 1.2.10

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DeepBlueR_1.2.10.tar.gz

StartedAt: 2017-10-17 22:34:01 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:38:25 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 264.2 seconds

RetCode: 0

Status:  OK

CheckDir: DeepBlueR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DeepBlueR_1.2.10.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.10’
* 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 1.912   0.02   6.141
* 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	0.776	0.008	1.837
deepblue_batch_export_results	1.912	0.020	6.141
deepblue_binning	0.044	0.000	0.920
deepblue_cache_status	0.004	0.000	0.003
deepblue_cancel_request	0.020	0.000	0.237
deepblue_chromosomes	0.044	0.008	0.286
deepblue_clear_cache	0.000	0.000	0.001
deepblue_collection_experiments_count	0.136	0.004	0.665
deepblue_commands	0.136	0.004	0.969
deepblue_count_gene_ontology_terms	0.248	0.000	0.816
deepblue_count_regions	0.036	0.000	0.960
deepblue_coverage	0.04	0.00	0.91
deepblue_delete_request_from_cache	0.004	0.000	0.004
deepblue_diff	0.424	0.000	0.927
deepblue_distinct_column_values	0.040	0.000	0.925
deepblue_download_request_data	0.944	0.000	2.829
deepblue_echo	0.012	0.000	0.229
deepblue_enrich_region_overlap	0.86	0.00	4.74
deepblue_enrich_regions_go_terms	0.112	0.000	1.278
deepblue_export_bed	0.296	0.012	2.758
deepblue_export_meta_data	0.256	0.000	0.632
deepblue_export_tab	0.116	0.004	1.575
deepblue_extend	0.056	0.004	0.563
deepblue_extract_ids	0.000	0.000	0.001
deepblue_extract_names	0.004	0.000	0.001
deepblue_faceting_experiments	0.036	0.000	0.639
deepblue_filter_regions	0.028	0.000	0.306
deepblue_find_motif	0.032	0.000	0.296
deepblue_flank	0.080	0.000	0.549
deepblue_get_biosource_children	0.024	0.000	0.265
deepblue_get_biosource_parents	0.016	0.000	0.244
deepblue_get_biosource_related	0.024	0.000	0.300
deepblue_get_biosource_synonyms	0.020	0.000	0.235
deepblue_get_experiments_by_query	0.052	0.000	0.344
deepblue_get_regions	0.044	0.000	0.956
deepblue_get_request_data	0.100	0.000	1.457
deepblue_info	0.032	0.000	0.253
deepblue_input_regions	0.016	0.000	0.539
deepblue_intersection	0.068	0.000	1.154
deepblue_is_biosource	0.012	0.000	0.252
deepblue_liftover	0.740	0.024	3.868
deepblue_list_annotations	0.032	0.000	0.299
deepblue_list_biosources	0.024	0.000	0.250
deepblue_list_cached_requests	0.004	0.000	0.002
deepblue_list_column_types	0.124	0.008	0.507
deepblue_list_epigenetic_marks	0.612	0.000	1.361
deepblue_list_experiments	0.252	0.000	0.734
deepblue_list_expressions	0.192	0.000	0.646
deepblue_list_gene_models	0.020	0.000	0.252
deepblue_list_genes	0.328	0.000	1.352
deepblue_list_genomes	0.020	0.000	0.263
deepblue_list_in_use	0.564	0.000	1.931
deepblue_list_projects	0.020	0.000	0.285
deepblue_list_recent_experiments	0.032	0.000	0.250
deepblue_list_requests	0.016	0.000	0.247
deepblue_list_samples	0.184	0.008	0.884
deepblue_list_similar_biosources	0.032	0.000	1.022
deepblue_list_similar_epigenetic_marks	0.032	0.000	0.329
deepblue_list_similar_experiments	0.024	0.000	2.345
deepblue_list_similar_genomes	0.020	0.000	0.297
deepblue_list_similar_projects	0.020	0.000	0.285
deepblue_list_similar_techniques	0.016	0.004	0.262
deepblue_list_techniques	0.032	0.000	0.267
deepblue_merge_queries	0.060	0.004	0.804
deepblue_meta_data_to_table	0.324	0.000	0.930
deepblue_name_to_id	0.076	0.000	0.766
deepblue_overlap	0.072	0.000	0.800
deepblue_preview_experiment	0.016	0.000	0.294
deepblue_query_cache	0.124	0.000	1.121
deepblue_query_experiment_type	0.052	0.000	1.740
deepblue_reset_options	0.000	0.000	0.001
deepblue_score_matrix	0.092	0.000	0.936
deepblue_search	0.064	0.004	0.608
deepblue_select_annotations	0.028	0.000	0.266
deepblue_select_column	0.524	0.000	1.394
deepblue_select_experiments	0.016	0.004	0.307
deepblue_select_expressions	0.036	0.000	0.355
deepblue_select_genes	0.032	0.000	0.385
deepblue_select_regions	0.1	0.0	1.4
deepblue_tiling_regions	0.012	0.004	0.296