Mac ARM64 build report for BioC 3.18 - CHECK results for DeepBlueR on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.3.1 Ventura	arm64	4.3.0 (2023-04-21) -- "Already Tomorrow"	3992
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_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/DeepBlueR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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 Ventura 13.3.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeepBlueR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepBlueR’ version ‘1.27.0’
* 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
* 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-3.18-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	0.058	0.008	0.237
deepblue_batch_export_results	0.280	0.035	2.918
deepblue_binning	0.034	0.002	0.152
deepblue_cache_status	0.001	0.001	0.002
deepblue_cancel_request	0.011	0.001	0.070
deepblue_chromosomes	0.040	0.002	0.100
deepblue_clear_cache	0.001	0.001	0.002
deepblue_collection_experiments_count	0.064	0.002	0.293
deepblue_commands	0.081	0.009	0.234
deepblue_count_gene_ontology_terms	0.070	0.007	0.167
deepblue_count_regions	0.027	0.003	0.145
deepblue_coverage	0.028	0.003	0.149
deepblue_delete_request_from_cache	0.002	0.001	0.003
deepblue_diff	0.106	0.026	0.253
deepblue_distinct_column_values	0.028	0.005	0.147
deepblue_download_request_data	0.233	0.022	1.258
deepblue_echo	0.011	0.002	0.070
deepblue_enrich_regions_go_terms	0.044	0.003	0.219
deepblue_enrich_regions_overlap	0.371	0.012	1.341
deepblue_export_bed	1.030	0.024	1.488
deepblue_export_meta_data	0.204	0.004	0.292
deepblue_export_tab	0.094	0.007	0.336
deepblue_extend	0.033	0.002	0.149
deepblue_extract_ids	0.001	0.000	0.001
deepblue_extract_names	0.001	0.001	0.001
deepblue_faceting_experiments	0.021	0.002	0.236
deepblue_filter_regions	0.016	0.002	0.074
deepblue_find_motif	0.017	0.001	0.074
deepblue_flank	0.030	0.002	0.149
deepblue_get_biosource_children	0.013	0.001	0.075
deepblue_get_biosource_parents	0.011	0.002	0.070
deepblue_get_biosource_related	0.014	0.001	0.084
deepblue_get_biosource_synonyms	0.012	0.001	0.071
deepblue_get_experiments_by_query	0.011	0.001	0.073
deepblue_get_regions	0.026	0.003	0.147
deepblue_get_request_data	0.049	0.004	0.913
deepblue_info	0.024	0.003	0.884
deepblue_input_regions	0.013	0.002	0.079
deepblue_intersection	0.042	0.004	0.908
deepblue_is_biosource	0.013	0.002	0.075
deepblue_liftover	0.251	0.034	3.940
deepblue_list_annotations	0.009	0.001	0.069
deepblue_list_biosources	0.010	0.001	0.068
deepblue_list_cached_requests	0.001	0.000	0.001
deepblue_list_column_types	0.028	0.001	0.116
deepblue_list_epigenetic_marks	0.249	0.004	0.399
deepblue_list_experiments	0.098	0.005	0.237
deepblue_list_expressions	0.085	0.010	0.187
deepblue_list_gene_models	0.014	0.002	0.076
deepblue_list_genes	0.169	0.019	0.365
deepblue_list_genomes	0.013	0.003	0.074
deepblue_list_in_use	0.237	0.025	0.904
deepblue_list_projects	0.063	0.003	0.139
deepblue_list_recent_experiments	0.022	0.001	0.086
deepblue_list_requests	0.016	0.001	0.078
deepblue_list_samples	0.089	0.018	0.248
deepblue_list_similar_biosources	0.018	0.002	0.252
deepblue_list_similar_epigenetic_marks	0.017	0.001	0.090
deepblue_list_similar_experiments	0.013	0.002	0.650
deepblue_list_similar_genomes	0.013	0.001	0.073
deepblue_list_similar_projects	0.013	0.001	0.070
deepblue_list_similar_techniques	0.013	0.001	0.071
deepblue_list_techniques	0.019	0.002	0.077
deepblue_merge_queries	0.043	0.003	0.217
deepblue_meta_data_to_table	0.186	0.006	0.342
deepblue_name_to_id	0.040	0.004	0.214
deepblue_overlap	0.046	0.003	0.224
deepblue_preview_experiment	0.012	0.001	0.078
deepblue_query_cache	0.056	0.005	0.290
deepblue_query_experiment_type	0.035	0.003	0.151
deepblue_reset_options	0.001	0.001	0.000
deepblue_score_matrix	0.031	0.002	0.147
deepblue_search	0.033	0.002	0.416
deepblue_select_annotations	0.018	0.001	0.075
deepblue_select_column	0.231	0.004	0.385
deepblue_select_experiments	0.015	0.001	0.077
deepblue_select_expressions	0.019	0.002	0.084
deepblue_select_genes	0.018	0.002	0.076
deepblue_select_regions	0.019	0.002	0.083
deepblue_tiling_regions	0.014	0.001	0.071

CHECK results for DeepBlueR on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings