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This page was generated on 2023-05-30 11:06:36 -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 palomino4


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: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DeepBlueR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings DeepBlueR_1.27.0.tar.gz
StartedAt: 2023-05-30 00:30:15 -0400 (Tue, 30 May 2023)
EndedAt: 2023-05-30 00:35:06 -0400 (Tue, 30 May 2023)
EllapsedTime: 290.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DeepBlueR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DeepBlueR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings DeepBlueR_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/DeepBlueR.Rcheck'
* using R version 4.3.0 RC (2023-04-18 r84287 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DeepBlueR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeepBlueR' version '1.27.0'
* 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 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 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
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
deepblue_batch_export_results 1.26    0.3    5.79
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/DeepBlueR.Rcheck/00check.log'
for details.



Installation output

DeepBlueR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL DeepBlueR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-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_aggregate0.080.000.67
deepblue_batch_export_results1.260.305.79
deepblue_binning0.010.000.42
deepblue_cache_status0.000.000.02
deepblue_cancel_request0.00.00.2
deepblue_chromosomes0.050.000.26
deepblue_clear_cache000
deepblue_collection_experiments_count0.090.000.55
deepblue_commands0.080.020.58
deepblue_count_gene_ontology_terms0.090.000.39
deepblue_count_regions0.020.010.44
deepblue_coverage0.030.030.45
deepblue_delete_request_from_cache000
deepblue_diff0.080.110.84
deepblue_distinct_column_values0.030.000.42
deepblue_download_request_data0.280.242.57
deepblue_echo0.030.000.22
deepblue_enrich_regions_go_terms0.080.000.65
deepblue_enrich_regions_overlap0.420.093.13
deepblue_export_bed0.200.061.84
deepblue_export_meta_data0.210.020.52
deepblue_export_tab0.120.010.92
deepblue_extend0.030.000.44
deepblue_extract_ids000
deepblue_extract_names000
deepblue_faceting_experiments0.010.000.44
deepblue_filter_regions0.020.000.22
deepblue_find_motif0.050.000.23
deepblue_flank0.010.000.42
deepblue_get_biosource_children0.030.000.24
deepblue_get_biosource_parents0.00.00.2
deepblue_get_biosource_related0.030.000.24
deepblue_get_biosource_synonyms0.020.000.21
deepblue_get_experiments_by_query0.020.020.22
deepblue_get_regions0.040.000.44
deepblue_get_request_data0.080.020.86
deepblue_info0.020.000.22
deepblue_input_regions0.010.000.23
deepblue_intersection0.080.000.66
deepblue_is_biosource0.030.000.22
deepblue_liftover0.530.013.08
deepblue_list_annotations0.030.000.21
deepblue_list_biosources0.030.000.22
deepblue_list_cached_requests000
deepblue_list_column_types0.070.000.35
deepblue_list_epigenetic_marks0.310.000.81
deepblue_list_experiments0.110.000.53
deepblue_list_expressions0.090.000.39
deepblue_list_gene_models0.00.00.2
deepblue_list_genes0.190.010.79
deepblue_list_genomes0.010.000.22
deepblue_list_in_use0.250.031.28
deepblue_list_projects0.010.000.22
deepblue_list_recent_experiments0.070.000.26
deepblue_list_requests0.010.000.22
deepblue_list_samples0.090.030.55
deepblue_list_similar_biosources0.040.000.40
deepblue_list_similar_epigenetic_marks0.030.000.24
deepblue_list_similar_experiments0.010.000.81
deepblue_list_similar_genomes0.030.000.22
deepblue_list_similar_projects0.020.000.22
deepblue_list_similar_techniques0.020.020.22
deepblue_list_techniques0.010.000.22
deepblue_merge_queries0.040.000.66
deepblue_meta_data_to_table0.240.020.75
deepblue_name_to_id0.030.010.67
deepblue_overlap0.070.000.68
deepblue_preview_experiment0.010.000.24
deepblue_query_cache0.070.000.90
deepblue_query_experiment_type0.040.000.47
deepblue_reset_options000
deepblue_score_matrix0.060.000.47
deepblue_search0.040.020.61
deepblue_select_annotations0.010.000.22
deepblue_select_column0.240.010.97
deepblue_select_experiments0.010.000.22
deepblue_select_expressions0.030.000.22
deepblue_select_genes0.020.000.21
deepblue_select_regions0.030.000.22
deepblue_tiling_regions0.030.000.22