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This page was generated on 2021-10-15 15:06:02 -0400 (Fri, 15 Oct 2021).

CHECK results for DeepBlueR on tokay2

To the developers/maintainers of the DeepBlueR package:
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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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeepBlueR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DeepBlueR_1.18.0.tar.gz
StartedAt: 2021-10-14 22:01:04 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 22:08:06 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 422.3 seconds
RetCode: 0
Status:   OK  
CheckDir: DeepBlueR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeepBlueR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DeepBlueR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DeepBlueR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
deepblue_batch_export_results 0.63   0.38    5.86
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/DeepBlueR.Rcheck/00check.log'
for details.



Installation output

DeepBlueR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DeepBlueR_1.18.0.tar.gz && rm -rf DeepBlueR.buildbin-libdir && mkdir DeepBlueR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeepBlueR.buildbin-libdir DeepBlueR_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DeepBlueR_1.18.0.zip && rm DeepBlueR_1.18.0.tar.gz DeepBlueR_1.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  522k  100  522k    0     0  1067k      0 --:--:-- --:--:-- --:--:-- 1068k

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* 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
  converting help for package 'DeepBlueR'
    finding HTML links ... done
    DeepBlueCommand-class                   html  
    deepblue_aggregate                      html  
    deepblue_batch_export_results           html  
    deepblue_binning                        html  
    deepblue_cache_status                   html  
    deepblue_cancel_request                 html  
    deepblue_chromosomes                    html  
    deepblue_clear_cache                    html  
    deepblue_collection_experiments_count   html  
    deepblue_column_types                   html  
    deepblue_commands                       html  
    deepblue_convert_to_df                  html  
    deepblue_convert_to_grange              html  
    deepblue_count_gene_ontology_terms      html  
    deepblue_count_regions                  html  
    deepblue_coverage                       html  
    deepblue_delete_request_from_cache      html  
    deepblue_diff                           html  
    deepblue_distinct_column_values         html  
    deepblue_download_request_data-DeepBlueCommand-method
                                            html  
    deepblue_download_request_data          html  
    deepblue_echo                           html  
    deepblue_enrich_regions_fast            html  
    deepblue_enrich_regions_go_terms        html  
    deepblue_enrich_regions_overlap         html  
    deepblue_export_bed                     html  
    deepblue_export_meta_data               html  
    deepblue_export_tab                     html  
    deepblue_extend                         html  
    deepblue_extract_ids                    html  
    deepblue_extract_names                  html  
    deepblue_faceting_experiments           html  
    deepblue_filter_regions                 html  
    deepblue_find_motif                     html  
    deepblue_flank                          html  
    deepblue_format_object_size             html  
    deepblue_get_biosource_children         html  
    deepblue_get_biosource_parents          html  
    deepblue_get_biosource_related          html  
    deepblue_get_biosource_synonyms         html  
    deepblue_get_db                         html  
    deepblue_get_experiments_by_query       html  
    deepblue_get_regions                    html  
    deepblue_get_request_data               html  
    deepblue_info                           html  
    deepblue_input_regions                  html  
    deepblue_intersection                   html  
    deepblue_is_biosource                   html  
    deepblue_liftover                       html  
    deepblue_list_annotations               html  
    deepblue_list_biosources                html  
    deepblue_list_cached_requests           html  
    deepblue_list_column_types              html  
    deepblue_list_epigenetic_marks          html  
    deepblue_list_experiments               html  
    deepblue_list_expressions               html  
    deepblue_list_gene_models               html  
    deepblue_list_genes                     html  
    deepblue_list_genomes                   html  
    deepblue_list_in_use                    html  
    deepblue_list_projects                  html  
    deepblue_list_recent_experiments        html  
    deepblue_list_requests                  html  
    deepblue_list_samples                   html  
    deepblue_list_similar_biosources        html  
    deepblue_list_similar_epigenetic_marks
                                            html  
    deepblue_list_similar_experiments       html  
    deepblue_list_similar_genomes           html  
    deepblue_list_similar_projects          html  
    deepblue_list_similar_techniques        html  
    deepblue_list_techniques                html  
    deepblue_merge_queries                  html  
    deepblue_meta_data_to_table             html  
    deepblue_name_to_id                     html  
    deepblue_options                        html  
    deepblue_overlap                        html  
    deepblue_parse_gtf                      html  
    deepblue_preview_experiment             html  
    deepblue_query_cache                    html  
    deepblue_query_experiment_type          html  
    deepblue_reset_options                  html  
    deepblue_score_matrix                   html  
    deepblue_search                         html  
    deepblue_select_annotations             html  
    deepblue_select_column                  html  
    deepblue_select_experiments             html  
    deepblue_select_expressions             html  
    deepblue_select_genes                   html  
    deepblue_select_regions                 html  
    deepblue_switch_get_request_data        html  
    deepblue_tiling_regions                 html  
    deepblue_wait_request                   html  
    show-DeepBlueCommand-method             html  
    xml.rpc                                 html  
** 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

install for x64

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'DeepBlueR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeepBlueR' as DeepBlueR_1.18.0.zip
* DONE (DeepBlueR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'DeepBlueR' successfully unpacked and MD5 sums checked

Tests output


Example timings

DeepBlueR.Rcheck/examples_i386/DeepBlueR-Ex.timings

nameusersystemelapsed
deepblue_aggregate0.110.010.87
deepblue_batch_export_results0.630.385.86
deepblue_binning0.680.011.19
deepblue_cache_status0.010.000.01
deepblue_cancel_request0.020.000.27
deepblue_chromosomes0.060.020.37
deepblue_clear_cache0.020.000.02
deepblue_collection_experiments_count0.120.000.59
deepblue_commands0.170.000.95
deepblue_count_gene_ontology_terms0.160.040.79
deepblue_count_regions0.060.000.56
deepblue_coverage0.050.020.57
deepblue_delete_request_from_cache0.010.000.01
deepblue_diff0.250.061.49
deepblue_distinct_column_values0.030.010.59
deepblue_download_request_data0.410.302.64
deepblue_echo0.000.000.27
deepblue_enrich_regions_go_terms0.080.030.86
deepblue_enrich_regions_overlap0.820.234.65
deepblue_export_bed0.380.273.11
deepblue_export_meta_data0.110.000.47
deepblue_export_tab0.200.001.17
deepblue_extend0.050.010.57
deepblue_extract_ids000
deepblue_extract_names000
deepblue_faceting_experiments0.050.000.56
deepblue_filter_regions0.020.000.27
deepblue_find_motif0.040.000.28
deepblue_flank0.050.000.56
deepblue_get_biosource_children0.010.000.28
deepblue_get_biosource_parents0.020.000.27
deepblue_get_biosource_related0.030.000.28
deepblue_get_biosource_synonyms0.010.000.26
deepblue_get_experiments_by_query0.020.000.27
deepblue_get_regions0.060.000.69
deepblue_get_request_data0.080.001.06
deepblue_info0.030.000.30
deepblue_input_regions0.020.000.26
deepblue_intersection0.050.000.81
deepblue_is_biosource0.020.000.27
deepblue_liftover0.790.354.76
deepblue_list_annotations0.050.000.30
deepblue_list_biosources0.010.000.28
deepblue_list_cached_requests0.020.000.01
deepblue_list_column_types0.110.000.47
deepblue_list_epigenetic_marks0.470.011.08
deepblue_list_experiments0.220.020.72
deepblue_list_expressions0.180.040.59
deepblue_list_gene_models0.050.000.29
deepblue_list_genes0.350.071.14
deepblue_list_genomes0.000.000.25
deepblue_list_in_use0.430.001.59
deepblue_list_projects0.030.000.28
deepblue_list_recent_experiments0.020.000.28
deepblue_list_requests0.030.000.28
deepblue_list_samples0.170.000.69
deepblue_list_similar_biosources0.030.000.45
deepblue_list_similar_epigenetic_marks0.050.000.30
deepblue_list_similar_experiments0.030.000.86
deepblue_list_similar_genomes0.020.000.27
deepblue_list_similar_projects0.020.000.27
deepblue_list_similar_techniques0.030.000.28
deepblue_list_techniques0.020.000.26
deepblue_merge_queries0.060.010.83
deepblue_meta_data_to_table0.140.000.75
deepblue_name_to_id0.080.000.83
deepblue_overlap0.110.000.86
deepblue_preview_experiment0.010.000.30
deepblue_query_cache0.110.001.07
deepblue_query_experiment_type0.060.020.60
deepblue_reset_options000
deepblue_score_matrix0.070.000.55
deepblue_search0.040.010.65
deepblue_select_annotations0.020.000.27
deepblue_select_column0.440.001.07
deepblue_select_experiments0.020.000.26
deepblue_select_expressions0.040.000.41
deepblue_select_genes0.020.040.40
deepblue_select_regions0.020.000.28
deepblue_tiling_regions0.030.000.29

DeepBlueR.Rcheck/examples_x64/DeepBlueR-Ex.timings

nameusersystemelapsed
deepblue_aggregate0.070.000.84
deepblue_batch_export_results0.580.344.30
deepblue_binning0.030.000.54
deepblue_cache_status0.000.020.01
deepblue_cancel_request0.030.000.27
deepblue_chromosomes0.090.000.34
deepblue_clear_cache000
deepblue_collection_experiments_count0.140.000.66
deepblue_commands0.180.000.89
deepblue_count_gene_ontology_terms0.120.000.64
deepblue_count_regions0.010.010.54
deepblue_coverage0.060.000.53
deepblue_delete_request_from_cache0.020.000.02
deepblue_diff0.200.050.73
deepblue_distinct_column_values0.020.010.55
deepblue_download_request_data1.040.303.31
deepblue_echo0.030.000.28
deepblue_enrich_regions_go_terms0.080.000.91
deepblue_enrich_regions_overlap0.810.024.48
deepblue_export_bed0.360.213.08
deepblue_export_meta_data0.110.000.47
deepblue_export_tab0.170.001.22
deepblue_extend0.080.000.56
deepblue_extract_ids000
deepblue_extract_names000
deepblue_faceting_experiments0.050.000.53
deepblue_filter_regions0.030.000.28
deepblue_find_motif0.030.000.29
deepblue_flank0.050.000.56
deepblue_get_biosource_children0.030.000.28
deepblue_get_biosource_parents0.000.020.26
deepblue_get_biosource_related0.030.000.29
deepblue_get_biosource_synonyms0.020.000.26
deepblue_get_experiments_by_query0.010.000.26
deepblue_get_regions0.030.000.55
deepblue_get_request_data0.070.011.06
deepblue_info0.030.000.30
deepblue_input_regions0.030.000.28
deepblue_intersection0.050.000.80
deepblue_is_biosource0.010.000.26
deepblue_liftover0.660.284.64
deepblue_list_annotations0.030.000.26
deepblue_list_biosources0.010.010.27
deepblue_list_cached_requests000
deepblue_list_column_types0.080.000.43
deepblue_list_epigenetic_marks0.500.001.11
deepblue_list_experiments0.210.000.72
deepblue_list_expressions0.180.000.56
deepblue_list_gene_models0.020.000.27
deepblue_list_genes0.360.021.11
deepblue_list_genomes0.010.000.33
deepblue_list_in_use0.460.061.62
deepblue_list_projects0.010.000.26
deepblue_list_recent_experiments0.030.000.28
deepblue_list_requests0.040.000.29
deepblue_list_samples0.180.020.71
deepblue_list_similar_biosources0.020.000.46
deepblue_list_similar_epigenetic_marks0.050.000.29
deepblue_list_similar_experiments0.030.000.86
deepblue_list_similar_genomes0.030.000.29
deepblue_list_similar_projects0.010.000.26
deepblue_list_similar_techniques0.030.000.28
deepblue_list_techniques0.020.000.27
deepblue_merge_queries0.080.000.86
deepblue_meta_data_to_table0.140.000.78
deepblue_name_to_id0.080.010.89
deepblue_overlap0.080.000.83
deepblue_preview_experiment0.030.000.28
deepblue_query_cache0.060.001.08
deepblue_query_experiment_type0.070.000.69
deepblue_reset_options000
deepblue_score_matrix0.060.001.02
deepblue_search0.060.000.64
deepblue_select_annotations0.020.000.26
deepblue_select_column0.450.021.08
deepblue_select_experiments0.020.000.28
deepblue_select_expressions0.040.000.41
deepblue_select_genes0.020.000.39
deepblue_select_regions0.020.000.28
deepblue_tiling_regions0.020.000.29