Multiple platform build/check report for BioC 3.12 - CHECK report for DeepBlueR on merida1

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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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/DeepBlueR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.16.0’
* 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 (user + system) or elapsed time > 5s
                   user system elapsed
deepblue_liftover 0.447  0.058   8.757
* 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-3.12-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.

Installation output

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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)

Tests output

Example timings

name	user	system	elapsed
deepblue_aggregate	0.086	0.010	1.300
deepblue_batch_export_results	0.450	0.024	3.586
deepblue_binning	0.043	0.002	0.520
deepblue_cache_status	0.003	0.001	0.004
deepblue_cancel_request	0.013	0.001	0.241
deepblue_chromosomes	0.070	0.003	0.316
deepblue_clear_cache	0.001	0.001	0.002
deepblue_collection_experiments_count	0.108	0.002	0.574
deepblue_commands	0.141	0.014	0.748
deepblue_count_gene_ontology_terms	0.134	0.013	0.595
deepblue_count_regions	0.040	0.005	0.521
deepblue_coverage	0.037	0.004	0.505
deepblue_delete_request_from_cache	0.003	0.002	0.005
deepblue_diff	0.805	0.035	1.308
deepblue_distinct_column_values	0.036	0.001	0.498
deepblue_download_request_data	0.183	0.014	1.758
deepblue_echo	0.014	0.001	0.250
deepblue_enrich_regions_go_terms	0.077	0.003	1.568
deepblue_enrich_regions_overlap	0.725	0.043	4.573
deepblue_export_bed	0.282	0.031	2.232
deepblue_export_meta_data	0.076	0.002	0.421
deepblue_export_tab	0.124	0.005	1.059
deepblue_extend	0.044	0.002	0.511
deepblue_extract_ids	0.000	0.000	0.001
deepblue_extract_names	0.001	0.000	0.001
deepblue_faceting_experiments	0.029	0.001	0.500
deepblue_filter_regions	0.031	0.002	0.263
deepblue_find_motif	0.031	0.001	0.265
deepblue_flank	0.050	0.002	0.515
deepblue_get_biosource_children	0.018	0.001	0.281
deepblue_get_biosource_parents	0.017	0.001	0.255
deepblue_get_biosource_related	0.020	0.001	0.259
deepblue_get_biosource_synonyms	0.020	0.001	0.253
deepblue_get_experiments_by_query	0.017	0.001	0.248
deepblue_get_regions	0.043	0.002	0.511
deepblue_get_request_data	0.079	0.003	1.023
deepblue_info	0.040	0.005	0.275
deepblue_input_regions	0.022	0.002	0.254
deepblue_intersection	0.064	0.003	0.775
deepblue_is_biosource	0.018	0.001	0.257
deepblue_liftover	0.447	0.058	8.757
deepblue_list_annotations	0.024	0.002	0.256
deepblue_list_biosources	0.018	0.001	0.252
deepblue_list_cached_requests	0.002	0.001	0.003
deepblue_list_column_types	0.070	0.002	0.416
deepblue_list_epigenetic_marks	0.436	0.006	1.011
deepblue_list_experiments	0.179	0.007	0.663
deepblue_list_expressions	0.174	0.021	0.542
deepblue_list_gene_models	0.020	0.003	0.274
deepblue_list_genes	0.328	0.039	1.052
deepblue_list_genomes	0.021	0.003	0.261
deepblue_list_in_use	0.526	0.014	1.580
deepblue_list_projects	0.015	0.001	0.252
deepblue_list_recent_experiments	0.028	0.001	0.263
deepblue_list_requests	0.020	0.002	0.274
deepblue_list_samples	0.158	0.020	0.662
deepblue_list_similar_biosources	0.025	0.002	0.422
deepblue_list_similar_epigenetic_marks	0.028	0.001	0.271
deepblue_list_similar_experiments	0.017	0.001	0.789
deepblue_list_similar_genomes	0.017	0.002	0.276
deepblue_list_similar_projects	0.017	0.001	0.260
deepblue_list_similar_techniques	0.020	0.001	0.248
deepblue_list_techniques	0.030	0.002	0.258
deepblue_merge_queries	0.074	0.003	0.777
deepblue_meta_data_to_table	0.120	0.004	0.739
deepblue_name_to_id	0.061	0.003	0.772
deepblue_overlap	0.081	0.003	0.786
deepblue_preview_experiment	0.019	0.001	0.258
deepblue_query_cache	0.098	0.004	1.035
deepblue_query_experiment_type	0.055	0.002	0.536
deepblue_reset_options	0.001	0.000	0.000
deepblue_score_matrix	0.057	0.002	0.542
deepblue_search	0.052	0.003	0.631
deepblue_select_annotations	0.027	0.001	0.267
deepblue_select_column	0.539	0.007	1.158
deepblue_select_experiments	0.023	0.001	0.256
deepblue_select_expressions	0.031	0.001	0.371
deepblue_select_genes	0.029	0.001	0.366
deepblue_select_regions	0.037	0.001	0.275
deepblue_tiling_regions	0.024	0.002	0.251

CHECK report for DeepBlueR on merida1

Summary

Command output

Installation output

Tests output

Example timings