Package: DeepBlueR

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DeepBlueR_1.13.0.tar.gz

StartedAt: 2020-01-16 03:34:27 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:41:01 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 394.9 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 --install=check:DeepBlueR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DeepBlueR_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DeepBlueR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.13.0’
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DeepBlueR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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	0.139	0.011	0.750
deepblue_batch_export_results	1.267	0.033	3.539
deepblue_binning	0.068	0.004	0.468
deepblue_cache_status	0.004	0.002	0.006
deepblue_cancel_request	0.022	0.002	0.224
deepblue_chromosomes	0.105	0.005	0.310
deepblue_clear_cache	0.002	0.002	0.004
deepblue_collection_experiments_count	0.184	0.016	0.642
deepblue_commands	0.567	0.365	0.763
deepblue_count_gene_ontology_terms	0.218	0.048	0.640
deepblue_count_regions	0.470	0.401	0.476
deepblue_coverage	0.072	0.014	0.485
deepblue_delete_request_from_cache	0.003	0.002	0.006
deepblue_diff	0.230	0.067	0.716
deepblue_distinct_column_values	0.065	0.008	0.468
deepblue_download_request_data	0.356	0.071	1.627
deepblue_echo	0.022	0.004	0.224
deepblue_enrich_regions_go_terms	0.111	0.020	0.733
deepblue_enrich_regions_overlap	1.013	0.023	4.174
deepblue_export_bed	0.327	0.020	1.958
deepblue_export_meta_data	0.126	0.005	0.427
deepblue_export_tab	0.153	0.009	0.954
deepblue_extend	0.072	0.004	0.475
deepblue_extract_ids	0.002	0.000	0.003
deepblue_extract_names	0.002	0.001	0.003
deepblue_faceting_experiments	0.060	0.009	0.520
deepblue_filter_regions	0.043	0.007	0.255
deepblue_find_motif	0.048	0.009	0.254
deepblue_flank	0.078	0.016	0.570
deepblue_get_biosource_children	0.034	0.005	0.244
deepblue_get_biosource_parents	0.018	0.003	0.219
deepblue_get_biosource_related	0.030	0.006	0.244
deepblue_get_biosource_synonyms	0.027	0.005	0.294
deepblue_get_experiments_by_query	0.027	0.006	0.231
deepblue_get_regions	0.071	0.013	0.484
deepblue_get_request_data	0.132	0.020	0.940
deepblue_info	0.072	0.016	0.287
deepblue_input_regions	0.034	0.007	0.283
deepblue_intersection	0.106	0.021	0.724
deepblue_is_biosource	0.027	0.005	0.228
deepblue_liftover	0.747	0.135	4.265
deepblue_list_annotations	0.032	0.002	0.233
deepblue_list_biosources	0.021	0.002	0.221
deepblue_list_cached_requests	0.002	0.002	0.004
deepblue_list_column_types	0.107	0.014	0.396
deepblue_list_epigenetic_marks	1.122	0.548	1.156
deepblue_list_experiments	0.719	0.526	0.665
deepblue_list_expressions	0.656	0.453	0.530
deepblue_list_gene_models	0.385	0.387	0.218
deepblue_list_genes	0.433	0.031	1.019
deepblue_list_genomes	0.419	0.400	0.223
deepblue_list_in_use	0.692	0.018	1.715
deepblue_list_projects	0.436	0.450	0.234
deepblue_list_recent_experiments	0.051	0.002	0.251
deepblue_list_requests	0.026	0.002	0.225
deepblue_list_samples	0.380	0.053	0.860
deepblue_list_similar_biosources	0.039	0.001	0.421
deepblue_list_similar_epigenetic_marks	0.036	0.002	0.250
deepblue_list_similar_experiments	0.029	0.001	0.816
deepblue_list_similar_genomes	0.026	0.001	0.224
deepblue_list_similar_projects	0.029	0.001	0.228
deepblue_list_similar_techniques	0.029	0.001	0.226
deepblue_list_techniques	0.041	0.002	0.242
deepblue_merge_queries	0.095	0.003	0.693
deepblue_meta_data_to_table	0.184	0.007	0.687
deepblue_name_to_id	0.082	0.007	0.705
deepblue_overlap	0.099	0.004	0.701
deepblue_preview_experiment	0.026	0.001	0.233
deepblue_query_cache	0.121	0.005	0.924
deepblue_query_experiment_type	0.074	0.003	0.482
deepblue_reset_options	0	0	0
deepblue_score_matrix	0.077	0.003	0.538
deepblue_search	0.075	0.004	0.639
deepblue_select_annotations	0.029	0.002	0.227
deepblue_select_column	0.681	0.036	1.180
deepblue_select_experiments	0.444	0.463	0.238
deepblue_select_expressions	0.040	0.002	0.332
deepblue_select_genes	0.033	0.002	0.328
deepblue_select_regions	0.051	0.001	0.255
deepblue_tiling_regions	0.032	0.001	0.230