Package: DeepBlueR

Version: 1.9.0

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_1.9.0.tar.gz

StartedAt: 2019-04-07 01:10:08 -0400 (Sun, 07 Apr 2019)

EndedAt: 2019-04-07 01:15:58 -0400 (Sun, 07 Apr 2019)

EllapsedTime: 350.3 seconds

RetCode: 0

Status:  OK

CheckDir: DeepBlueR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DeepBlueR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.0’
* 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
Examples with CPU or elapsed time > 5s
                                 user system elapsed
deepblue_enrich_regions_overlap 5.386  1.132   4.526
* 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-3.9-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DeepBlueR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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	0.121	0.023	0.785
deepblue_batch_export_results	1.217	0.039	3.605
deepblue_binning	0.063	0.003	0.531
deepblue_cache_status	0.003	0.002	0.005
deepblue_cancel_request	0.025	0.002	0.232
deepblue_chromosomes	0.142	0.043	0.345
deepblue_clear_cache	0.009	0.007	0.004
deepblue_collection_experiments_count	0.609	0.523	0.582
deepblue_commands	0.661	0.518	0.802
deepblue_count_gene_ontology_terms	1.130	0.561	1.191
deepblue_count_regions	0.379	0.343	0.493
deepblue_coverage	0.050	0.003	0.477
deepblue_delete_request_from_cache	0.003	0.002	0.006
deepblue_diff	0.978	0.956	0.653
deepblue_distinct_column_values	0.193	0.152	0.490
deepblue_download_request_data	0.227	0.015	1.630
deepblue_echo	0.013	0.002	0.220
deepblue_enrich_regions_go_terms	0.089	0.004	0.734
deepblue_enrich_regions_overlap	5.386	1.132	4.526
deepblue_export_bed	0.292	0.019	2.032
deepblue_export_meta_data	0.401	0.136	0.457
deepblue_export_tab	0.485	0.375	1.023
deepblue_extend	0.066	0.002	0.493
deepblue_extract_ids	0.002	0.000	0.002
deepblue_extract_names	0.001	0.000	0.001
deepblue_faceting_experiments	0.038	0.002	0.482
deepblue_filter_regions	0.034	0.001	0.258
deepblue_find_motif	0.037	0.001	0.261
deepblue_flank	0.070	0.002	0.488
deepblue_get_biosource_children	0.042	0.012	0.244
deepblue_get_biosource_parents	0.412	0.436	0.229
deepblue_get_biosource_related	0.045	0.016	0.265
deepblue_get_biosource_synonyms	0.424	0.460	0.254
deepblue_get_experiments_by_query	1.806	0.244	0.234
deepblue_get_regions	0.061	0.002	0.949
deepblue_get_request_data	0.119	0.005	1.468
deepblue_info	0.102	0.051	0.289
deepblue_input_regions	0.434	0.473	0.242
deepblue_intersection	0.085	0.004	0.743
deepblue_is_biosource	0.024	0.002	0.244
deepblue_liftover	0.666	0.101	4.055
deepblue_list_annotations	0.051	0.015	0.258
deepblue_list_biosources	0.422	0.434	0.249
deepblue_list_cached_requests	0.003	0.002	0.012
deepblue_list_column_types	0.125	0.023	0.414
deepblue_list_epigenetic_marks	1.073	0.446	1.180
deepblue_list_experiments	0.673	0.430	0.708
deepblue_list_expressions	2.323	0.123	0.556
deepblue_list_gene_models	0.417	0.424	0.258
deepblue_list_genes	0.994	0.539	1.316
deepblue_list_genomes	1.912	0.301	0.264
deepblue_list_in_use	2.196	0.573	1.913
deepblue_list_projects	1.405	0.296	0.263
deepblue_list_recent_experiments	1.799	0.297	0.257
deepblue_list_requests	0.024	0.001	0.230
deepblue_list_samples	0.363	0.144	0.718
deepblue_list_similar_biosources	0.312	0.302	0.407
deepblue_list_similar_epigenetic_marks	0.438	0.438	0.261
deepblue_list_similar_experiments	0.472	0.406	0.783
deepblue_list_similar_genomes	0.039	0.012	0.244
deepblue_list_similar_projects	0.434	0.446	0.233
deepblue_list_similar_techniques	0.411	0.451	0.241
deepblue_list_techniques	0.508	0.515	0.269
deepblue_merge_queries	0.562	0.559	0.742
deepblue_meta_data_to_table	0.874	0.802	0.769
deepblue_name_to_id	0.387	0.374	0.726
deepblue_overlap	0.108	0.004	0.747
deepblue_preview_experiment	0.026	0.001	0.257
deepblue_query_cache	0.116	0.005	1.044
deepblue_query_experiment_type	0.072	0.003	0.509
deepblue_reset_options	0.000	0.000	0.001
deepblue_score_matrix	0.058	0.003	0.493
deepblue_search	0.105	0.038	0.649
deepblue_select_annotations	0.502	0.502	0.250
deepblue_select_column	0.739	0.063	1.233
deepblue_select_experiments	0.468	0.513	0.255
deepblue_select_expressions	0.034	0.002	0.344
deepblue_select_genes	0.044	0.001	0.370
deepblue_select_regions	0.048	0.002	0.258
deepblue_tiling_regions	0.032	0.002	0.252