Back to Multiple platform build/check report for BioC 3.13
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).

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 461/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeepBlueR 1.18.0  (landing page)
Felipe Albrecht , Markus List
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/DeepBlueR
git_branch: RELEASE_3_13
git_last_commit: 96a5591
git_last_commit_date: 2021-05-19 12:21:41 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DeepBlueR
Version: 1.18.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DeepBlueR_1.18.0.tar.gz
StartedAt: 2021-10-14 09:30:29 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:34:37 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 248.3 seconds
RetCode: 0
Status:   OK  
CheckDir: DeepBlueR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DeepBlueR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/DeepBlueR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.18.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
deepblue_enrich_regions_overlap 0.504  0.096    5.04
* 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-3.13-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.



Installation output

DeepBlueR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL DeepBlueR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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_aggregate0.0890.0000.912
deepblue_batch_export_results1.1710.0354.012
deepblue_binning0.0400.0000.608
deepblue_cache_status0.0030.0000.003
deepblue_cancel_request0.0160.0000.299
deepblue_chromosomes0.0580.0040.345
deepblue_clear_cache0.0020.0000.002
deepblue_collection_experiments_count0.0700.0040.616
deepblue_commands0.0750.0121.316
deepblue_count_gene_ontology_terms0.0990.0040.565
deepblue_count_regions0.0240.0150.606
deepblue_coverage0.0360.0080.554
deepblue_delete_request_from_cache0.0040.0000.004
deepblue_diff0.1110.0080.694
deepblue_distinct_column_values0.0330.0040.601
deepblue_download_request_data0.1630.0161.544
deepblue_echo0.0120.0000.294
deepblue_enrich_regions_go_terms0.0630.0040.898
deepblue_enrich_regions_overlap0.5040.0965.040
deepblue_export_bed0.2190.0122.173
deepblue_export_meta_data0.0610.0030.460
deepblue_export_tab0.0930.0041.155
deepblue_extend0.0400.0000.589
deepblue_extract_ids0.0000.0010.002
deepblue_extract_names0.0000.0020.001
deepblue_faceting_experiments0.0220.0000.657
deepblue_filter_regions0.0190.0000.259
deepblue_find_motif0.0280.0000.311
deepblue_flank0.0520.0000.603
deepblue_get_biosource_children0.0210.0000.311
deepblue_get_biosource_parents0.0140.0040.302
deepblue_get_biosource_related0.0210.0000.316
deepblue_get_biosource_synonyms0.0140.0040.302
deepblue_get_experiments_by_query0.0180.0000.301
deepblue_get_regions0.0370.0040.595
deepblue_get_request_data0.0540.0081.236
deepblue_info0.0290.0040.315
deepblue_input_regions0.0140.0000.310
deepblue_intersection0.0550.0000.829
deepblue_is_biosource0.0170.0000.297
deepblue_liftover0.4260.0563.292
deepblue_list_annotations0.0220.0000.307
deepblue_list_biosources0.0150.0040.325
deepblue_list_cached_requests0.0030.0000.003
deepblue_list_column_types0.0460.0010.436
deepblue_list_epigenetic_marks0.3080.0031.599
deepblue_list_experiments0.1490.0000.794
deepblue_list_expressions0.0820.0010.605
deepblue_list_gene_models0.0120.0040.300
deepblue_list_genes0.1770.0141.805
deepblue_list_genomes0.0210.0000.310
deepblue_list_in_use0.2080.0001.805
deepblue_list_projects0.0160.0000.261
deepblue_list_recent_experiments0.0330.0000.320
deepblue_list_requests0.0170.0040.310
deepblue_list_samples0.1870.0241.075
deepblue_list_similar_biosources0.0250.0000.423
deepblue_list_similar_epigenetic_marks0.0200.0000.275
deepblue_list_similar_experiments0.0170.0000.829
deepblue_list_similar_genomes0.0160.0000.258
deepblue_list_similar_projects0.0190.0000.313
deepblue_list_similar_techniques0.0150.0040.302
deepblue_list_techniques0.0220.0040.343
deepblue_merge_queries0.0560.0000.868
deepblue_meta_data_to_table0.1160.0040.792
deepblue_name_to_id0.0570.0000.892
deepblue_overlap0.0700.0040.889
deepblue_preview_experiment0.0190.0000.303
deepblue_query_cache0.0640.0001.154
deepblue_query_experiment_type0.0490.0000.618
deepblue_reset_options0.0000.0010.000
deepblue_score_matrix0.0470.0030.616
deepblue_search0.0540.0000.673
deepblue_select_annotations0.0280.0000.269
deepblue_select_column0.3100.0001.605
deepblue_select_experiments0.0200.0000.304
deepblue_select_expressions0.0260.0000.270
deepblue_select_genes0.0260.0000.280
deepblue_select_regions0.0250.0020.311
deepblue_tiling_regions0.0210.0020.307