Multiple platform build/check report for BioC 3.11 - CHECK report for DeepBlueR on machv2

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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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DeepBlueR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.14.0’
* 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.

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	0.097	0.004	0.697
deepblue_batch_export_results	0.494	0.026	3.516
deepblue_binning	0.053	0.002	0.468
deepblue_cache_status	0.003	0.002	0.004
deepblue_cancel_request	0.019	0.001	0.224
deepblue_chromosomes	0.088	0.005	0.289
deepblue_clear_cache	0.002	0.001	0.002
deepblue_collection_experiments_count	0.153	0.011	0.618
deepblue_commands	0.189	0.027	0.747
deepblue_count_gene_ontology_terms	0.156	0.016	0.558
deepblue_count_regions	0.048	0.004	0.449
deepblue_coverage	0.051	0.006	0.453
deepblue_delete_request_from_cache	0.002	0.002	0.004
deepblue_diff	0.821	0.036	1.253
deepblue_distinct_column_values	0.044	0.001	0.437
deepblue_download_request_data	0.238	0.014	1.432
deepblue_echo	0.018	0.001	0.226
deepblue_enrich_regions_go_terms	0.081	0.003	0.681
deepblue_enrich_regions_overlap	0.801	0.049	3.726
deepblue_export_bed	0.314	0.033	2.038
deepblue_export_meta_data	0.108	0.003	0.401
deepblue_export_tab	0.130	0.006	0.930
deepblue_extend	0.052	0.002	0.449
deepblue_extract_ids	0.001	0.000	0.002
deepblue_extract_names	0.001	0.000	0.002
deepblue_faceting_experiments	0.042	0.002	0.474
deepblue_filter_regions	0.031	0.002	0.238
deepblue_find_motif	0.035	0.001	0.264
deepblue_flank	0.059	0.002	0.465
deepblue_get_biosource_children	0.024	0.001	0.225
deepblue_get_biosource_parents	0.019	0.001	0.231
deepblue_get_biosource_related	0.025	0.002	0.274
deepblue_get_biosource_synonyms	0.023	0.002	0.240
deepblue_get_experiments_by_query	0.021	0.001	0.221
deepblue_get_regions	0.046	0.002	0.463
deepblue_get_request_data	0.103	0.003	0.883
deepblue_info	0.049	0.005	0.263
deepblue_input_regions	0.023	0.001	0.229
deepblue_intersection	0.081	0.002	0.737
deepblue_is_biosource	0.021	0.001	0.219
deepblue_liftover	0.632	0.079	4.328
deepblue_list_annotations	0.030	0.002	0.239
deepblue_list_biosources	0.024	0.001	0.243
deepblue_list_cached_requests	0.003	0.001	0.003
deepblue_list_column_types	0.087	0.001	0.377
deepblue_list_epigenetic_marks	0.660	0.005	1.159
deepblue_list_experiments	0.237	0.006	0.648
deepblue_list_expressions	0.218	0.026	0.541
deepblue_list_gene_models	0.022	0.002	0.231
deepblue_list_genes	0.426	0.025	1.033
deepblue_list_genomes	0.020	0.001	0.222
deepblue_list_in_use	0.536	0.003	1.567
deepblue_list_projects	0.020	0.001	0.237
deepblue_list_recent_experiments	0.041	0.001	0.237
deepblue_list_requests	0.021	0.001	0.225
deepblue_list_samples	0.210	0.029	0.659
deepblue_list_similar_biosources	0.035	0.001	0.410
deepblue_list_similar_epigenetic_marks	0.030	0.001	0.256
deepblue_list_similar_experiments	0.022	0.001	0.808
deepblue_list_similar_genomes	0.022	0.001	0.222
deepblue_list_similar_projects	0.022	0.001	0.212
deepblue_list_similar_techniques	0.022	0.001	0.223
deepblue_list_techniques	0.036	0.002	0.235
deepblue_merge_queries	0.083	0.002	0.703
deepblue_meta_data_to_table	0.157	0.008	0.651
deepblue_name_to_id	0.066	0.003	0.666
deepblue_overlap	0.086	0.003	0.682
deepblue_preview_experiment	0.020	0.001	0.237
deepblue_query_cache	0.104	0.004	0.941
deepblue_query_experiment_type	0.057	0.003	0.599
deepblue_reset_options	0.000	0.001	0.001
deepblue_score_matrix	0.061	0.003	1.001
deepblue_search	0.112	0.005	0.642
deepblue_select_annotations	0.033	0.001	0.241
deepblue_select_column	0.545	0.003	1.055
deepblue_select_experiments	0.023	0.001	0.241
deepblue_select_expressions	0.036	0.001	0.320
deepblue_select_genes	0.034	0.001	0.322
deepblue_select_regions	0.040	0.001	0.244
deepblue_tiling_regions	0.026	0.001	0.220

CHECK report for DeepBlueR on machv2

Summary

Command output

Installation output

Tests output

Example timings