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This page was generated on 2022-01-26 11:11:20 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
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? here 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 471/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeepBlueR 1.21.0  (landing page)
Felipe Albrecht , Markus List
Snapshot Date: 2022-01-25 13:55:17 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/DeepBlueR
git_branch: master
git_last_commit: 340e089
git_last_commit_date: 2021-10-26 12:28:59 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DeepBlueR
Version: 1.21.0
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_1.21.0.tar.gz
StartedAt: 2022-01-26 00:02:27 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 00:09:09 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 401.9 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/DeepBlueR.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.21.0’
* 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 ... 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-3.15-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/4.2/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

DeepBlueR.Rcheck/DeepBlueR-Ex.timings

nameusersystemelapsed
deepblue_aggregate0.1130.0100.815
deepblue_batch_export_results1.2230.0454.172
deepblue_binning0.0630.0020.526
deepblue_cache_status0.0040.0010.004
deepblue_cancel_request0.0220.0000.259
deepblue_chromosomes0.0830.0030.322
deepblue_clear_cache0.0010.0010.003
deepblue_collection_experiments_count0.1520.0020.679
deepblue_commands0.1680.0090.752
deepblue_count_gene_ontology_terms0.1730.0150.648
deepblue_count_regions0.0530.0050.536
deepblue_coverage0.0570.0060.520
deepblue_delete_request_from_cache0.0030.0010.004
deepblue_diff0.1810.0360.697
deepblue_distinct_column_values0.0520.0060.540
deepblue_download_request_data0.3020.0241.807
deepblue_echo0.0190.0010.249
deepblue_enrich_regions_go_terms0.0830.0020.801
deepblue_enrich_regions_overlap0.8960.0114.209
deepblue_export_bed0.3090.0352.252
deepblue_export_meta_data0.1130.0120.478
deepblue_export_tab0.1690.0181.169
deepblue_extend0.0680.0070.558
deepblue_extract_ids0.0010.0000.001
deepblue_extract_names0.0010.0010.002
deepblue_faceting_experiments0.0410.0050.517
deepblue_filter_regions0.0300.0040.289
deepblue_find_motif0.0380.0040.271
deepblue_flank0.0710.0080.564
deepblue_get_biosource_children0.0270.0030.264
deepblue_get_biosource_parents0.0220.0020.279
deepblue_get_biosource_related0.0280.0030.277
deepblue_get_biosource_synonyms0.0250.0020.256
deepblue_get_experiments_by_query0.0220.0020.258
deepblue_get_regions0.0910.0050.891
deepblue_get_request_data0.0820.0031.010
deepblue_info0.0490.0040.296
deepblue_input_regions0.0260.0010.265
deepblue_intersection0.0910.0020.786
deepblue_is_biosource0.0210.0010.260
deepblue_liftover0.6120.0492.484
deepblue_list_annotations0.0310.0020.260
deepblue_list_biosources0.0250.0010.263
deepblue_list_cached_requests0.0020.0010.004
deepblue_list_column_types0.0940.0020.453
deepblue_list_epigenetic_marks0.6570.0051.230
deepblue_list_experiments0.2360.0020.729
deepblue_list_expressions0.2190.0020.588
deepblue_list_gene_models0.0230.0000.254
deepblue_list_genes0.4380.0061.153
deepblue_list_genomes0.0220.0010.276
deepblue_list_in_use0.6090.0051.757
deepblue_list_projects0.0190.0010.256
deepblue_list_recent_experiments0.0340.0010.263
deepblue_list_requests0.0220.0010.263
deepblue_list_samples0.2210.0120.732
deepblue_list_similar_biosources0.0340.0010.433
deepblue_list_similar_epigenetic_marks0.0310.0010.288
deepblue_list_similar_experiments0.0260.0010.845
deepblue_list_similar_genomes0.0230.0010.251
deepblue_list_similar_projects0.0250.0000.260
deepblue_list_similar_techniques0.0250.0010.257
deepblue_list_techniques0.0420.0020.274
deepblue_merge_queries0.0880.0020.799
deepblue_meta_data_to_table0.1670.0040.748
deepblue_name_to_id0.0780.0020.792
deepblue_overlap0.1060.0020.812
deepblue_preview_experiment0.0230.0010.269
deepblue_query_cache0.1160.0031.096
deepblue_query_experiment_type0.0720.0020.541
deepblue_reset_options0.0010.0010.001
deepblue_score_matrix0.0640.0020.578
deepblue_search0.0650.0020.640
deepblue_select_annotations0.0350.0010.271
deepblue_select_column0.6130.0071.211
deepblue_select_experiments0.030.000.28
deepblue_select_expressions0.0400.0010.385
deepblue_select_genes0.0380.0010.380
deepblue_select_regions0.0450.0010.280
deepblue_tiling_regions0.0280.0010.254