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This page was generated on 2023-02-07 11:06:45 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

CHECK results for DeepBlueR on merida1


To the developers/maintainers of the DeepBlueR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DeepBlueR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 486/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeepBlueR 1.25.1  (landing page)
Felipe Albrecht , Markus List , Quirin Manz
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/DeepBlueR
git_branch: master
git_last_commit: 950d10c
git_last_commit_date: 2023-01-10 05:24:28 -0500 (Tue, 10 Jan 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DeepBlueR
Version: 1.25.1
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_1.25.1.tar.gz
StartedAt: 2023-02-07 00:26:20 -0500 (Tue, 07 Feb 2023)
EndedAt: 2023-02-07 00:35:49 -0500 (Tue, 07 Feb 2023)
EllapsedTime: 568.8 seconds
RetCode: 0
Status:   OK  
CheckDir: DeepBlueR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/DeepBlueR.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeepBlueR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepBlueR’ version ‘1.25.1’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
deepblue_batch_export_results 0.513  0.047   5.634
* 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-3.17-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.



Installation output

DeepBlueR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/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

DeepBlueR.Rcheck/DeepBlueR-Ex.timings

nameusersystemelapsed
deepblue_aggregate0.1090.0040.791
deepblue_batch_export_results0.5130.0475.634
deepblue_binning0.0980.0090.549
deepblue_cache_status0.0030.0010.004
deepblue_cancel_request0.0210.0010.244
deepblue_chromosomes0.0950.0020.327
deepblue_clear_cache0.0020.0010.002
deepblue_collection_experiments_count0.1630.0020.702
deepblue_commands0.1790.0100.733
deepblue_count_gene_ontology_terms0.1880.0020.646
deepblue_count_regions0.0540.0030.524
deepblue_coverage0.0570.0070.513
deepblue_delete_request_from_cache0.0030.0020.005
deepblue_diff0.1990.0400.688
deepblue_distinct_column_values0.0580.0070.508
deepblue_download_request_data0.2880.0381.863
deepblue_echo0.0200.0020.242
deepblue_enrich_regions_go_terms0.0970.0110.782
deepblue_enrich_regions_overlap1.0340.0874.336
deepblue_export_bed0.3150.0142.180
deepblue_export_meta_data0.5110.0050.897
deepblue_export_tab0.2070.0051.116
deepblue_extend0.0680.0010.521
deepblue_extract_ids0.0010.0000.002
deepblue_extract_names0.0010.0010.001
deepblue_faceting_experiments0.0460.0010.505
deepblue_filter_regions0.0370.0010.263
deepblue_find_motif0.0370.0010.263
deepblue_flank0.0690.0020.518
deepblue_get_biosource_children0.0270.0020.257
deepblue_get_biosource_parents0.0230.0010.269
deepblue_get_biosource_related0.0280.0010.256
deepblue_get_biosource_synonyms0.0240.0010.246
deepblue_get_experiments_by_query0.0230.0010.248
deepblue_get_regions0.0580.0010.501
deepblue_get_request_data0.1260.0041.019
deepblue_info0.0520.0020.280
deepblue_input_regions0.0250.0010.260
deepblue_intersection0.0870.0020.754
deepblue_is_biosource0.0230.0010.244
deepblue_liftover0.6740.0492.688
deepblue_list_annotations0.0350.0020.261
deepblue_list_biosources0.0270.0010.249
deepblue_list_cached_requests0.0020.0010.003
deepblue_list_column_types0.1030.0010.431
deepblue_list_epigenetic_marks0.7660.0061.453
deepblue_list_experiments0.2580.0040.738
deepblue_list_expressions0.2340.0030.582
deepblue_list_gene_models0.0250.0010.250
deepblue_list_genes0.5070.0091.223
deepblue_list_genomes0.0250.0010.255
deepblue_list_in_use0.6930.0041.891
deepblue_list_projects0.0270.0010.255
deepblue_list_recent_experiments0.0470.0010.272
deepblue_list_requests0.0280.0010.253
deepblue_list_samples0.2280.0120.743
deepblue_list_similar_biosources0.0400.0010.440
deepblue_list_similar_epigenetic_marks0.0370.0010.272
deepblue_list_similar_experiments0.0290.0010.784
deepblue_list_similar_genomes0.0240.0010.254
deepblue_list_similar_projects0.0250.0010.257
deepblue_list_similar_techniques0.0280.0010.261
deepblue_list_techniques0.0420.0020.267
deepblue_merge_queries0.0960.0031.253
deepblue_meta_data_to_table0.6210.0061.273
deepblue_name_to_id0.0790.0020.756
deepblue_overlap0.1000.0030.801
deepblue_preview_experiment0.0220.0010.277
deepblue_query_cache0.1170.0041.008
deepblue_query_experiment_type0.0740.0020.525
deepblue_reset_options0.0000.0010.001
deepblue_score_matrix0.0700.0020.530
deepblue_search0.0750.0020.629
deepblue_select_annotations0.0350.0010.265
deepblue_select_column0.6630.0041.320
deepblue_select_experiments0.0320.0010.262
deepblue_select_expressions0.0400.0010.365
deepblue_select_genes0.0400.0010.369
deepblue_select_regions0.0450.0010.277
deepblue_tiling_regions0.0310.0000.254