Package: DeepBlueR

Version: 1.9.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DeepBlueR_1.9.0.tar.gz

StartedAt: 2019-04-07 00:06:31 -0400 (Sun, 07 Apr 2019)

EndedAt: 2019-04-07 00:11:40 -0400 (Sun, 07 Apr 2019)

EllapsedTime: 308.5 seconds

RetCode: 0

Status:  OK

CheckDir: DeepBlueR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DeepBlueR_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DeepBlueR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.0’
* 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 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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DeepBlueR
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DeepBlueR’ ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DeepBlueR)

name	user	system	elapsed
deepblue_aggregate	0.075	0.004	0.887
deepblue_batch_export_results	1.010	0.004	4.057
deepblue_binning	0.039	0.004	0.592
deepblue_cache_status	0.002	0.000	0.002
deepblue_cancel_request	0.017	0.000	0.245
deepblue_chromosomes	0.809	0.005	0.668
deepblue_clear_cache	0.008	0.000	0.002
deepblue_collection_experiments_count	1.791	0.006	0.870
deepblue_commands	0.125	0.008	0.718
deepblue_count_gene_ontology_terms	2.257	0.044	1.242
deepblue_count_regions	0.047	0.000	0.573
deepblue_coverage	0.040	0.000	0.558
deepblue_delete_request_from_cache	0.002	0.000	0.002
deepblue_diff	1.628	0.009	1.025
deepblue_distinct_column_values	0.037	0.000	0.766
deepblue_download_request_data	0.192	0.004	1.673
deepblue_echo	0.020	0.000	0.246
deepblue_enrich_regions_go_terms	0.068	0.000	0.956
deepblue_enrich_regions_overlap	2.833	0.036	4.334
deepblue_export_bed	0.219	0.004	2.474
deepblue_export_meta_data	2.237	0.024	0.824
deepblue_export_tab	0.109	0.008	1.158
deepblue_extend	0.050	0.000	0.594
deepblue_extract_ids	0.001	0.000	0.002
deepblue_extract_names	0.001	0.000	0.001
deepblue_faceting_experiments	0.036	0.000	0.490
deepblue_filter_regions	0.024	0.000	0.271
deepblue_find_motif	0.030	0.000	0.303
deepblue_flank	0.044	0.000	0.569
deepblue_get_biosource_children	0.759	0.000	0.459
deepblue_get_biosource_parents	0.024	0.000	0.277
deepblue_get_biosource_related	0.696	0.000	0.403
deepblue_get_biosource_synonyms	0.742	0.006	0.408
deepblue_get_experiments_by_query	0.026	0.000	0.359
deepblue_get_regions	0.035	0.004	0.612
deepblue_get_request_data	0.073	0.000	1.097
deepblue_info	0.761	0.004	0.439
deepblue_input_regions	0.026	0.000	0.300
deepblue_intersection	0.062	0.004	0.935
deepblue_is_biosource	0.011	0.000	0.240
deepblue_liftover	0.489	0.024	3.644
deepblue_list_annotations	0.717	0.008	0.449
deepblue_list_biosources	0.046	0.000	0.303
deepblue_list_cached_requests	0.002	0.000	0.002
deepblue_list_column_types	1.627	0.012	0.815
deepblue_list_epigenetic_marks	2.044	0.002	1.383
deepblue_list_experiments	1.803	0.009	1.038
deepblue_list_expressions	1.772	0.004	0.903
deepblue_list_gene_models	0.764	0.007	0.477
deepblue_list_genes	1.892	0.039	1.372
deepblue_list_genomes	0.784	0.005	0.452
deepblue_list_in_use	2.349	0.019	1.941
deepblue_list_projects	0.747	0.013	0.470
deepblue_list_recent_experiments	0.032	0.000	0.271
deepblue_list_requests	0.015	0.000	0.244
deepblue_list_samples	0.892	0.008	0.869
deepblue_list_similar_biosources	0.735	0.001	0.640
deepblue_list_similar_epigenetic_marks	0.798	0.000	0.464
deepblue_list_similar_experiments	0.029	0.004	0.842
deepblue_list_similar_genomes	0.759	0.001	0.475
deepblue_list_similar_projects	0.746	0.004	0.477
deepblue_list_similar_techniques	0.803	0.005	0.498
deepblue_list_techniques	0.757	0.004	0.490
deepblue_merge_queries	0.085	0.004	0.864
deepblue_meta_data_to_table	3.151	0.034	1.621
deepblue_name_to_id	0.055	0.000	0.874
deepblue_overlap	0.069	0.000	0.987
deepblue_preview_experiment	0.016	0.000	0.255
deepblue_query_cache	0.082	0.000	1.120
deepblue_query_experiment_type	0.052	0.000	0.568
deepblue_reset_options	0	0	0
deepblue_score_matrix	0.051	0.000	0.564
deepblue_search	0.775	0.008	0.751
deepblue_select_annotations	0.034	0.001	0.300
deepblue_select_column	1.218	0.003	1.164
deepblue_select_experiments	0.022	0.000	0.287
deepblue_select_expressions	0.029	0.000	0.382
deepblue_select_genes	0.029	0.000	0.373
deepblue_select_regions	0.034	0.000	0.283
deepblue_tiling_regions	0.014	0.008	0.275