Mac ARM64 build report for BioC 3.17 - CHECK results for DeepBlueR on kjohnson2

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson2	macOS 12.6.1 Monterey	arm64	4.3.0 RC (2023-04-13 r84266) -- "Already Tomorrow"	4269
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_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DeepBlueR.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeepBlueR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepBlueR’ version ‘1.26.0’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    v0.99.0 Initial Bioconductor submission
  Cannot process chunk/lines:
    v1.0.0 Bioconductor 3.4 release
  Cannot process chunk/lines:
    v1.2.0 Bioconductor 3.5 release
  Cannot process chunk/lines:
    v1.4.0 Bioconductor 3.6 release
  Cannot process chunk/lines:
    v1.4.1 Bugfixes following changes in the DeepBlue API
* 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 startup messages can be suppressed ... 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 0.476  0.081    9.47
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/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	0.068	0.010	0.817
deepblue_batch_export_results	0.358	0.053	3.094
deepblue_binning	0.043	0.005	0.537
deepblue_cache_status	0.002	0.002	0.006
deepblue_cancel_request	0.016	0.002	0.258
deepblue_chromosomes	0.053	0.005	0.319
deepblue_clear_cache	0.001	0.001	0.003
deepblue_collection_experiments_count	0.084	0.004	0.643
deepblue_commands	0.109	0.012	0.750
deepblue_count_gene_ontology_terms	0.097	0.006	0.501
deepblue_count_regions	0.032	0.005	0.551
deepblue_coverage	0.036	0.006	0.536
deepblue_delete_request_from_cache	0.002	0.002	0.009
deepblue_diff	0.130	0.045	0.735
deepblue_distinct_column_values	0.035	0.006	0.545
deepblue_download_request_data	0.229	0.031	1.721
deepblue_echo	0.013	0.002	0.257
deepblue_enrich_regions_go_terms	0.052	0.005	0.787
deepblue_enrich_regions_overlap	0.483	0.019	3.610
deepblue_export_bed	0.856	0.040	3.125
deepblue_export_meta_data	0.279	0.006	0.776
deepblue_export_tab	0.119	0.011	1.135
deepblue_extend	0.039	0.003	0.530
deepblue_extract_ids	0.000	0.000	0.003
deepblue_extract_names	0.001	0.000	0.001
deepblue_faceting_experiments	0.026	0.002	0.552
deepblue_filter_regions	0.021	0.002	0.268
deepblue_find_motif	0.024	0.002	0.271
deepblue_flank	0.040	0.003	0.546
deepblue_get_biosource_children	0.016	0.002	0.273
deepblue_get_biosource_parents	0.015	0.002	0.260
deepblue_get_biosource_related	0.017	0.003	0.274
deepblue_get_biosource_synonyms	0.016	0.002	0.258
deepblue_get_experiments_by_query	0.014	0.002	0.437
deepblue_get_regions	0.032	0.004	0.536
deepblue_get_request_data	0.058	0.006	1.015
deepblue_info	0.033	0.006	0.295
deepblue_input_regions	0.017	0.002	0.274
deepblue_intersection	0.056	0.006	0.794
deepblue_is_biosource	0.014	0.003	0.256
deepblue_liftover	0.476	0.081	9.470
deepblue_list_annotations	0.020	0.002	0.272
deepblue_list_biosources	0.017	0.002	0.255
deepblue_list_cached_requests	0.002	0.002	0.004
deepblue_list_column_types	0.057	0.004	0.434
deepblue_list_epigenetic_marks	0.390	0.013	1.184
deepblue_list_experiments	0.135	0.010	0.695
deepblue_list_expressions	0.155	0.010	0.610
deepblue_list_gene_models	0.016	0.002	0.262
deepblue_list_genes	0.258	0.008	1.085
deepblue_list_genomes	0.016	0.002	0.257
deepblue_list_in_use	0.320	0.007	1.566
deepblue_list_projects	0.016	0.002	0.285
deepblue_list_recent_experiments	0.029	0.002	0.284
deepblue_list_requests	0.016	0.003	0.261
deepblue_list_samples	0.123	0.022	0.714
deepblue_list_similar_biosources	0.021	0.002	0.448
deepblue_list_similar_epigenetic_marks	0.061	0.005	0.360
deepblue_list_similar_experiments	0.016	0.002	0.843
deepblue_list_similar_genomes	0.015	0.002	0.257
deepblue_list_similar_projects	0.017	0.002	0.264
deepblue_list_similar_techniques	0.017	0.002	0.606
deepblue_list_techniques	0.026	0.003	0.275
deepblue_merge_queries	0.056	0.005	0.874
deepblue_meta_data_to_table	0.271	0.010	1.002
deepblue_name_to_id	0.051	0.005	0.784
deepblue_overlap	0.059	0.005	0.804
deepblue_preview_experiment	0.013	0.001	0.254
deepblue_query_cache	0.070	0.007	1.044
deepblue_query_experiment_type	0.045	0.004	0.548
deepblue_reset_options	0.000	0.001	0.003
deepblue_score_matrix	0.036	0.004	0.519
deepblue_search	0.038	0.004	0.615
deepblue_select_annotations	0.021	0.002	0.268
deepblue_select_column	0.341	0.011	1.128
deepblue_select_experiments	0.019	0.002	0.263
deepblue_select_expressions	0.022	0.002	0.276
deepblue_select_genes	0.023	0.002	0.270
deepblue_select_regions	0.024	0.002	0.272
deepblue_tiling_regions	0.017	0.002	0.255

CHECK results for DeepBlueR on kjohnson2

Summary

Command output

Installation output

Tests output

Example timings