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This page was generated on 2023-05-30 11:05:43 -0400 (Tue, 30 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.0 RC (2023-04-18 r84287) -- "Already Tomorrow" 4587
palomino4Windows Server 2022 Datacenterx644.3.0 RC (2023-04-18 r84287 ucrt) -- "Already Tomorrow" 4336
lconwaymacOS 12.6.5 Montereyx86_644.3.0 RC (2023-04-13 r84266) -- "Already Tomorrow" 4337
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 nebbiolo2


To the developers/maintainers of the DeepBlueR package:
- 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 Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 503/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeepBlueR 1.27.0  (landing page)
Felipe Albrecht , Markus List , Quirin Manz
Snapshot Date: 2023-05-29 14:00:06 -0400 (Mon, 29 May 2023)
git_url: https://git.bioconductor.org/packages/DeepBlueR
git_branch: devel
git_last_commit: 76840cb
git_last_commit_date: 2023-04-25 10:48:12 -0400 (Tue, 25 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DeepBlueR
Version: 1.27.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DeepBlueR_1.27.0.tar.gz
StartedAt: 2023-05-29 20:29:19 -0400 (Mon, 29 May 2023)
EndedAt: 2023-05-29 20:44:27 -0400 (Mon, 29 May 2023)
EllapsedTime: 907.7 seconds
RetCode: 0
Status:   OK  
CheckDir: DeepBlueR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DeepBlueR_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DeepBlueR.Rcheck’
* using R version 4.3.0 RC (2023-04-18 r84287)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘DeepBlueR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepBlueR’ version ‘1.27.0’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    v0.99.0 Initial Bioconductor submission
  Cannot process chunk/lines:
    v1.0.0 Bioconductor 3.4 release
  Cannot process chunk/lines:
    v1.2.0 Bioconductor 3.5 release
  Cannot process chunk/lines:
    v1.4.0 Bioconductor 3.6 release
  Cannot process chunk/lines:
    v1.4.1 Bugfixes following changes in the DeepBlue API
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ...
  ‘DeepBlueR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.



Installation output

DeepBlueR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL DeepBlueR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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_aggregate0.0960.0200.952
deepblue_batch_export_results1.2950.2484.387
deepblue_binning0.0330.0000.625
deepblue_cache_status0.0040.0000.004
deepblue_cancel_request0.0230.0000.312
deepblue_chromosomes0.0830.0000.390
deepblue_clear_cache0.0020.0000.002
deepblue_collection_experiments_count0.0730.0000.561
deepblue_commands0.1130.0081.414
deepblue_count_gene_ontology_terms0.1020.0000.398
deepblue_count_regions0.0200.0110.563
deepblue_coverage0.0510.0120.628
deepblue_delete_request_from_cache0.0040.0000.004
deepblue_diff0.1550.0400.780
deepblue_distinct_column_values0.0380.0080.628
deepblue_download_request_data0.2430.0161.662
deepblue_echo0.0100.0000.298
deepblue_enrich_regions_go_terms0.0620.0120.926
deepblue_enrich_regions_overlap0.4440.0644.873
deepblue_export_bed0.2630.0602.310
deepblue_export_meta_data0.2120.0120.634
deepblue_export_tab0.0930.0111.354
deepblue_extend0.0280.0080.600
deepblue_extract_ids000
deepblue_extract_names000
deepblue_faceting_experiments0.0210.0070.688
deepblue_filter_regions0.0290.0010.322
deepblue_find_motif0.0320.0000.321
deepblue_flank0.0550.0000.618
deepblue_get_biosource_children0.0230.0000.318
deepblue_get_biosource_parents0.0190.0000.309
deepblue_get_biosource_related0.0280.0000.326
deepblue_get_biosource_synonyms0.0130.0060.311
deepblue_get_experiments_by_query0.010.000.30
deepblue_get_regions0.0260.0000.585
deepblue_get_request_data0.0420.0001.175
deepblue_info0.0340.0000.328
deepblue_input_regions0.0200.0000.325
deepblue_intersection0.0590.0080.906
deepblue_is_biosource0.0240.0000.312
deepblue_liftover0.3910.0482.830
deepblue_list_annotations0.0170.0000.308
deepblue_list_biosources0.0160.0000.305
deepblue_list_cached_requests0.0030.0000.002
deepblue_list_column_types0.0780.0000.480
deepblue_list_epigenetic_marks0.3280.0121.636
deepblue_list_experiments0.0990.0120.763
deepblue_list_expressions0.0970.0000.615
deepblue_list_gene_models0.0150.0000.304
deepblue_list_genes0.2920.0002.034
deepblue_list_genomes0.0160.0000.313
deepblue_list_in_use0.3690.0802.092
deepblue_list_projects0.0120.0080.313
deepblue_list_recent_experiments0.0290.0040.326
deepblue_list_requests0.0220.0000.274
deepblue_list_samples0.1520.0081.046
deepblue_list_similar_biosources0.0160.0040.472
deepblue_list_similar_epigenetic_marks0.0150.0040.320
deepblue_list_similar_experiments0.0150.0040.848
deepblue_list_similar_genomes0.0100.0040.302
deepblue_list_similar_projects0.0190.0040.331
deepblue_list_similar_techniques0.0280.0040.327
deepblue_list_techniques0.0430.0040.336
deepblue_merge_queries0.0950.0041.056
deepblue_meta_data_to_table0.2600.0360.972
deepblue_name_to_id0.0430.0191.048
deepblue_overlap0.0750.0080.932
deepblue_preview_experiment0.0190.0040.322
deepblue_query_cache0.1000.0121.181
deepblue_query_experiment_type0.0780.0010.676
deepblue_reset_options0.0010.0000.000
deepblue_score_matrix0.0460.0040.665
deepblue_search0.0390.0040.649
deepblue_select_annotations0.0160.0040.315
deepblue_select_column0.3130.0121.649
deepblue_select_experiments0.0150.0000.310
deepblue_select_expressions0.0270.0000.280
deepblue_select_genes0.0420.0000.455
deepblue_select_regions0.0370.0120.342
deepblue_tiling_regions0.0260.0000.318