Multiple platform build/check report for BioC 3.15 - CHECK results for DeepBlueR on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 20.04.4 LTS)	x86_64	R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"	4164
riesling1	Windows Server 2019 Standard	x64	R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"	4059
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences"	4001
merida1	macOS 10.14.6 Mojave	x86_64	R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"	4118
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeepBlueR_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/DeepBlueR.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.21.0’
* 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-3.15-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DeepBlueR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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	0.113	0.010	0.815
deepblue_batch_export_results	1.223	0.045	4.172
deepblue_binning	0.063	0.002	0.526
deepblue_cache_status	0.004	0.001	0.004
deepblue_cancel_request	0.022	0.000	0.259
deepblue_chromosomes	0.083	0.003	0.322
deepblue_clear_cache	0.001	0.001	0.003
deepblue_collection_experiments_count	0.152	0.002	0.679
deepblue_commands	0.168	0.009	0.752
deepblue_count_gene_ontology_terms	0.173	0.015	0.648
deepblue_count_regions	0.053	0.005	0.536
deepblue_coverage	0.057	0.006	0.520
deepblue_delete_request_from_cache	0.003	0.001	0.004
deepblue_diff	0.181	0.036	0.697
deepblue_distinct_column_values	0.052	0.006	0.540
deepblue_download_request_data	0.302	0.024	1.807
deepblue_echo	0.019	0.001	0.249
deepblue_enrich_regions_go_terms	0.083	0.002	0.801
deepblue_enrich_regions_overlap	0.896	0.011	4.209
deepblue_export_bed	0.309	0.035	2.252
deepblue_export_meta_data	0.113	0.012	0.478
deepblue_export_tab	0.169	0.018	1.169
deepblue_extend	0.068	0.007	0.558
deepblue_extract_ids	0.001	0.000	0.001
deepblue_extract_names	0.001	0.001	0.002
deepblue_faceting_experiments	0.041	0.005	0.517
deepblue_filter_regions	0.030	0.004	0.289
deepblue_find_motif	0.038	0.004	0.271
deepblue_flank	0.071	0.008	0.564
deepblue_get_biosource_children	0.027	0.003	0.264
deepblue_get_biosource_parents	0.022	0.002	0.279
deepblue_get_biosource_related	0.028	0.003	0.277
deepblue_get_biosource_synonyms	0.025	0.002	0.256
deepblue_get_experiments_by_query	0.022	0.002	0.258
deepblue_get_regions	0.091	0.005	0.891
deepblue_get_request_data	0.082	0.003	1.010
deepblue_info	0.049	0.004	0.296
deepblue_input_regions	0.026	0.001	0.265
deepblue_intersection	0.091	0.002	0.786
deepblue_is_biosource	0.021	0.001	0.260
deepblue_liftover	0.612	0.049	2.484
deepblue_list_annotations	0.031	0.002	0.260
deepblue_list_biosources	0.025	0.001	0.263
deepblue_list_cached_requests	0.002	0.001	0.004
deepblue_list_column_types	0.094	0.002	0.453
deepblue_list_epigenetic_marks	0.657	0.005	1.230
deepblue_list_experiments	0.236	0.002	0.729
deepblue_list_expressions	0.219	0.002	0.588
deepblue_list_gene_models	0.023	0.000	0.254
deepblue_list_genes	0.438	0.006	1.153
deepblue_list_genomes	0.022	0.001	0.276
deepblue_list_in_use	0.609	0.005	1.757
deepblue_list_projects	0.019	0.001	0.256
deepblue_list_recent_experiments	0.034	0.001	0.263
deepblue_list_requests	0.022	0.001	0.263
deepblue_list_samples	0.221	0.012	0.732
deepblue_list_similar_biosources	0.034	0.001	0.433
deepblue_list_similar_epigenetic_marks	0.031	0.001	0.288
deepblue_list_similar_experiments	0.026	0.001	0.845
deepblue_list_similar_genomes	0.023	0.001	0.251
deepblue_list_similar_projects	0.025	0.000	0.260
deepblue_list_similar_techniques	0.025	0.001	0.257
deepblue_list_techniques	0.042	0.002	0.274
deepblue_merge_queries	0.088	0.002	0.799
deepblue_meta_data_to_table	0.167	0.004	0.748
deepblue_name_to_id	0.078	0.002	0.792
deepblue_overlap	0.106	0.002	0.812
deepblue_preview_experiment	0.023	0.001	0.269
deepblue_query_cache	0.116	0.003	1.096
deepblue_query_experiment_type	0.072	0.002	0.541
deepblue_reset_options	0.001	0.001	0.001
deepblue_score_matrix	0.064	0.002	0.578
deepblue_search	0.065	0.002	0.640
deepblue_select_annotations	0.035	0.001	0.271
deepblue_select_column	0.613	0.007	1.211
deepblue_select_experiments	0.03	0.00	0.28
deepblue_select_expressions	0.040	0.001	0.385
deepblue_select_genes	0.038	0.001	0.380
deepblue_select_regions	0.045	0.001	0.280
deepblue_tiling_regions	0.028	0.001	0.254

CHECK results for DeepBlueR on merida1

Summary

Command output

Installation output

Tests output

Example timings