Multiple platform build/check report for BioC 3.17 - CHECK results for DeepBlueR on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.2 LTS)	x86_64	4.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow"	4617
palomino3	Windows Server 2022 Datacenter	x64	4.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow"	4368
merida1	macOS 12.6.4 Monterey	x86_64	4.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow"	4326
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/meat/DeepBlueR.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84257)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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 0.717  0.108   9.222
* 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/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-x86_64/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	0.116	0.017	0.796
deepblue_batch_export_results	0.539	0.066	3.741
deepblue_binning	0.068	0.003	0.520
deepblue_cache_status	0.004	0.002	0.005
deepblue_cancel_request	0.023	0.001	0.240
deepblue_chromosomes	0.097	0.006	0.323
deepblue_clear_cache	0.002	0.002	0.003
deepblue_collection_experiments_count	0.172	0.004	0.671
deepblue_commands	0.195	0.027	0.761
deepblue_count_gene_ontology_terms	0.189	0.012	0.533
deepblue_count_regions	0.055	0.008	0.497
deepblue_coverage	0.061	0.009	0.505
deepblue_delete_request_from_cache	0.003	0.003	0.006
deepblue_diff	0.205	0.058	0.696
deepblue_distinct_column_values	0.064	0.009	0.688
deepblue_download_request_data	0.356	0.038	1.942
deepblue_echo	0.019	0.002	0.242
deepblue_enrich_regions_go_terms	0.095	0.004	0.747
deepblue_enrich_regions_overlap	0.996	0.016	3.760
deepblue_export_bed	1.141	0.046	2.986
deepblue_export_meta_data	0.505	0.007	0.913
deepblue_export_tab	0.205	0.009	1.097
deepblue_extend	0.069	0.003	0.503
deepblue_extract_ids	0.001	0.001	0.002
deepblue_extract_names	0.001	0.000	0.002
deepblue_faceting_experiments	0.045	0.003	0.505
deepblue_filter_regions	0.037	0.002	0.259
deepblue_find_motif	0.041	0.002	0.259
deepblue_flank	0.070	0.003	0.504
deepblue_get_biosource_children	0.027	0.002	0.253
deepblue_get_biosource_parents	0.024	0.002	0.241
deepblue_get_biosource_related	0.027	0.002	0.251
deepblue_get_biosource_synonyms	0.024	0.002	0.245
deepblue_get_experiments_by_query	0.021	0.002	0.241
deepblue_get_regions	0.057	0.003	0.498
deepblue_get_request_data	0.096	0.006	0.969
deepblue_info	0.054	0.009	0.374
deepblue_input_regions	0.026	0.002	0.260
deepblue_intersection	0.092	0.007	1.201
deepblue_is_biosource	0.023	0.003	0.246
deepblue_liftover	0.717	0.108	9.222
deepblue_list_annotations	0.036	0.003	0.376
deepblue_list_biosources	0.027	0.001	0.245
deepblue_list_cached_requests	0.002	0.002	0.005
deepblue_list_column_types	0.100	0.002	0.446
deepblue_list_epigenetic_marks	0.774	0.011	1.636
deepblue_list_experiments	0.281	0.016	0.768
deepblue_list_expressions	0.279	0.017	0.682
deepblue_list_gene_models	0.024	0.002	0.257
deepblue_list_genes	0.471	0.010	1.180
deepblue_list_genomes	0.025	0.002	0.251
deepblue_list_in_use	0.679	0.009	1.792
deepblue_list_projects	0.027	0.003	0.255
deepblue_list_recent_experiments	0.046	0.002	0.267
deepblue_list_requests	0.028	0.002	0.251
deepblue_list_samples	0.244	0.060	0.777
deepblue_list_similar_biosources	0.041	0.002	0.443
deepblue_list_similar_epigenetic_marks	0.081	0.005	0.317
deepblue_list_similar_experiments	0.026	0.001	0.818
deepblue_list_similar_genomes	0.026	0.002	0.243
deepblue_list_similar_projects	0.026	0.001	0.257
deepblue_list_similar_techniques	0.026	0.002	0.249
deepblue_list_techniques	0.041	0.003	0.260
deepblue_merge_queries	0.094	0.004	0.755
deepblue_meta_data_to_table	0.497	0.014	1.107
deepblue_name_to_id	0.079	0.006	0.744
deepblue_overlap	0.105	0.004	0.760
deepblue_preview_experiment	0.024	0.002	0.262
deepblue_query_cache	0.120	0.005	0.998
deepblue_query_experiment_type	0.074	0.004	0.857
deepblue_reset_options	0.000	0.000	0.001
deepblue_score_matrix	0.068	0.003	1.012
deepblue_search	0.077	0.006	0.621
deepblue_select_annotations	0.038	0.002	0.257
deepblue_select_column	0.707	0.014	1.413
deepblue_select_experiments	0.036	0.003	0.270
deepblue_select_expressions	0.038	0.002	0.270
deepblue_select_genes	0.039	0.002	0.257
deepblue_select_regions	0.046	0.002	0.268
deepblue_tiling_regions	0.029	0.002	0.246

CHECK results for DeepBlueR on merida1

Summary

Command output

Installation output

Tests output

Example timings