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This page was generated on 2022-01-17 11:05:34 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 nebbiolo1


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 471/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeepBlueR 1.21.0  (landing page)
Felipe Albrecht , Markus List
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings DeepBlueR_1.21.0.tar.gz
StartedAt: 2022-01-16 18:51:59 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 18:56:11 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 251.8 seconds
RetCode: 0
Status:   OK  
CheckDir: DeepBlueR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings DeepBlueR_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/DeepBlueR.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.



Installation output

DeepBlueR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL DeepBlueR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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_aggregate0.0700.0040.957
deepblue_batch_export_results0.9850.0433.790
deepblue_binning0.0480.0000.621
deepblue_cache_status0.0050.0000.005
deepblue_cancel_request0.0180.0040.303
deepblue_chromosomes0.0490.0080.343
deepblue_clear_cache0.0010.0000.001
deepblue_collection_experiments_count0.1050.0000.674
deepblue_commands0.0990.0081.326
deepblue_count_gene_ontology_terms0.0770.0080.360
deepblue_count_regions0.0260.0080.591
deepblue_coverage0.0300.0080.586
deepblue_delete_request_from_cache0.0030.0000.003
deepblue_diff0.1530.0040.726
deepblue_distinct_column_values0.0390.0040.611
deepblue_download_request_data0.2540.0121.642
deepblue_echo0.0160.0040.302
deepblue_enrich_regions_go_terms0.0590.0040.893
deepblue_enrich_regions_overlap0.4700.0124.999
deepblue_export_bed0.1840.0282.091
deepblue_export_meta_data0.0810.0040.478
deepblue_export_tab0.1300.0091.214
deepblue_extend0.0490.0080.668
deepblue_extract_ids0.0010.0000.001
deepblue_extract_names0.0010.0000.001
deepblue_faceting_experiments0.0300.0040.665
deepblue_filter_regions0.0160.0070.306
deepblue_find_motif0.0210.0040.266
deepblue_flank0.0340.0120.597
deepblue_get_biosource_children0.0230.0000.311
deepblue_get_biosource_parents0.0190.0000.305
deepblue_get_biosource_related0.0200.0040.310
deepblue_get_biosource_synonyms0.0220.0000.305
deepblue_get_experiments_by_query0.0190.0000.299
deepblue_get_regions0.0950.0000.643
deepblue_get_request_data0.0600.0001.203
deepblue_info0.0310.0040.326
deepblue_input_regions0.0200.0000.313
deepblue_intersection0.0610.0000.870
deepblue_is_biosource0.0190.0000.299
deepblue_liftover0.4030.0112.920
deepblue_list_annotations0.0260.0000.309
deepblue_list_biosources0.0200.0010.298
deepblue_list_cached_requests0.0010.0030.003
deepblue_list_column_types0.0650.0000.457
deepblue_list_epigenetic_marks0.3320.0151.622
deepblue_list_experiments0.1060.0000.744
deepblue_list_expressions0.0840.0040.593
deepblue_list_gene_models0.0170.0000.298
deepblue_list_genes0.1790.0561.713
deepblue_list_genomes0.0160.0000.297
deepblue_list_in_use0.2890.0922.047
deepblue_list_projects0.0180.0000.304
deepblue_list_recent_experiments0.0280.0040.319
deepblue_list_requests0.0150.0000.304
deepblue_list_samples0.1120.0130.869
deepblue_list_similar_biosources0.0260.0000.462
deepblue_list_similar_epigenetic_marks0.0160.0070.281
deepblue_list_similar_experiments0.0180.0070.890
deepblue_list_similar_genomes0.0180.0000.301
deepblue_list_similar_projects0.0100.0120.263
deepblue_list_similar_techniques0.0210.0000.261
deepblue_list_techniques0.0250.0080.314
deepblue_merge_queries0.0690.0040.887
deepblue_meta_data_to_table0.1180.0120.789
deepblue_name_to_id0.0500.0110.893
deepblue_overlap0.0800.0040.898
deepblue_preview_experiment0.0190.0000.306
deepblue_query_cache0.0850.0071.298
deepblue_query_experiment_type0.0490.0010.618
deepblue_reset_options000
deepblue_score_matrix0.0400.0030.606
deepblue_search0.0450.0010.664
deepblue_select_annotations0.0190.0030.310
deepblue_select_column0.2960.0431.665
deepblue_select_experiments0.0140.0040.312
deepblue_select_expressions0.0280.0040.274
deepblue_select_genes0.0290.0000.271
deepblue_select_regions0.0290.0000.271
deepblue_tiling_regions0.0160.0000.300