Multiple platform build/check report for BioC 3.16 - CHECK results for DeepBlueR on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4502
palomino4	Windows Server 2022 Datacenter	x64	4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"	4282
lconway	macOS 12.5.1 Monterey	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4310
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*

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/DeepBlueR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘1.24.1’
* 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-3.16-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.

Installation output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DeepBlueR
###
##############################################################################
##############################################################################


* 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	0.053	0.004	0.918
deepblue_batch_export_results	0.242	0.031	3.053
deepblue_binning	0.032	0.004	0.616
deepblue_cache_status	0.002	0.001	0.004
deepblue_cancel_request	0.011	0.002	0.297
deepblue_chromosomes	0.035	0.007	0.332
deepblue_clear_cache	0.001	0.001	0.003
deepblue_collection_experiments_count	0.060	0.009	0.628
deepblue_commands	0.078	0.015	1.528
deepblue_count_gene_ontology_terms	0.075	0.010	0.592
deepblue_count_regions	0.025	0.004	0.588
deepblue_coverage	0.026	0.004	0.545
deepblue_delete_request_from_cache	0.002	0.002	0.004
deepblue_diff	0.116	0.025	0.716
deepblue_distinct_column_values	0.025	0.002	0.615
deepblue_download_request_data	0.119	0.012	1.522
deepblue_echo	0.011	0.001	0.297
deepblue_enrich_regions_go_terms	0.037	0.003	0.878
deepblue_enrich_regions_overlap	0.356	0.014	4.638
deepblue_export_bed	0.184	0.026	2.073
deepblue_export_meta_data	0.210	0.004	0.612
deepblue_export_tab	0.085	0.006	1.159
deepblue_extend	0.027	0.002	0.582
deepblue_extract_ids	0.001	0.000	0.001
deepblue_extract_names	0.000	0.000	0.001
deepblue_faceting_experiments	0.017	0.002	0.643
deepblue_filter_regions	0.014	0.001	0.305
deepblue_find_motif	0.020	0.002	0.304
deepblue_flank	0.035	0.002	0.547
deepblue_get_biosource_children	0.014	0.001	0.302
deepblue_get_biosource_parents	0.011	0.001	0.301
deepblue_get_biosource_related	0.016	0.002	0.313
deepblue_get_biosource_synonyms	0.015	0.001	0.304
deepblue_get_experiments_by_query	0.013	0.001	0.304
deepblue_get_regions	0.029	0.002	0.588
deepblue_get_request_data	0.051	0.003	1.206
deepblue_info	0.025	0.004	0.315
deepblue_input_regions	0.014	0.002	0.307
deepblue_intersection	0.046	0.003	0.872
deepblue_is_biosource	0.011	0.001	0.294
deepblue_liftover	1.093	0.048	3.742
deepblue_list_annotations	0.018	0.001	0.308
deepblue_list_biosources	0.014	0.001	0.302
deepblue_list_cached_requests	0.001	0.001	0.003
deepblue_list_column_types	0.037	0.002	0.447
deepblue_list_epigenetic_marks	0.234	0.003	1.411
deepblue_list_experiments	0.096	0.005	0.743
deepblue_list_expressions	0.113	0.009	0.636
deepblue_list_gene_models	0.015	0.002	0.305
deepblue_list_genes	0.220	0.018	1.628
deepblue_list_genomes	0.014	0.001	0.300
deepblue_list_in_use	0.195	0.002	1.613
deepblue_list_projects	0.014	0.001	0.259
deepblue_list_recent_experiments	0.021	0.001	0.330
deepblue_list_requests	0.015	0.001	0.306
deepblue_list_samples	0.083	0.014	1.081
deepblue_list_similar_biosources	0.017	0.001	0.453
deepblue_list_similar_epigenetic_marks	0.016	0.001	0.320
deepblue_list_similar_experiments	0.013	0.001	0.869
deepblue_list_similar_genomes	0.014	0.001	0.258
deepblue_list_similar_projects	0.012	0.001	0.258
deepblue_list_similar_techniques	0.012	0.001	0.296
deepblue_list_techniques	0.020	0.001	0.267
deepblue_merge_queries	0.046	0.003	0.875
deepblue_meta_data_to_table	0.179	0.006	0.850
deepblue_name_to_id	0.037	0.003	0.877
deepblue_overlap	0.090	0.004	0.914
deepblue_preview_experiment	0.010	0.001	0.300
deepblue_query_cache	0.054	0.004	1.149
deepblue_query_experiment_type	0.032	0.002	0.609
deepblue_reset_options	0	0	0
deepblue_score_matrix	0.033	0.002	0.611
deepblue_search	0.025	0.003	0.640
deepblue_select_annotations	0.018	0.001	0.265
deepblue_select_column	0.232	0.002	1.533
deepblue_select_experiments	0.014	0.001	0.259
deepblue_select_expressions	0.017	0.001	0.154
deepblue_select_genes	0.016	0.001	0.308
deepblue_select_regions	0.024	0.001	0.315
deepblue_tiling_regions	0.011	0.001	0.301

CHECK results for DeepBlueR on lconway

Summary

Command output

Installation output

Tests output

Example timings