BioC 3.4: CHECK report for DeepBlueR on zin1

Package: DeepBlueR

Version: 0.99.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DeepBlueR_0.99.2.tar.gz

StartedAt: 2016-09-20 05:25:09 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:27:16 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 127.6 seconds

RetCode: 0

Status:  OK

CheckDir: DeepBlueR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DeepBlueR_0.99.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DeepBlueR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘0.99.2’
* 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 loading without being on the library search path ... 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 ... OK
* 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 installed files from ‘inst/doc’ ... 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: OK

* installing *source* package ‘DeepBlueR’ ...
** R
** demo
** inst
** preparing 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
* DONE (DeepBlueR)

name	user	system	elapsed
deepblue_aggregate	0.068	0.000	1.507
deepblue_batch_export_results	0.140	0.012	2.478
deepblue_cancel_request	0.016	0.000	0.385
deepblue_chromosomes	0.116	0.000	0.466
deepblue_collection_experiments_count	0.048	0.000	0.423
deepblue_commands	0.892	0.020	2.285
deepblue_count_regions	0.028	0.004	0.944
deepblue_coverage	0.036	0.000	0.935
deepblue_download_request_data	0.096	0.004	2.038
deepblue_echo	0.012	0.000	0.363
deepblue_extend	0.044	0.004	1.006
deepblue_extract_ids	0.004	0.000	0.002
deepblue_extract_names	0.000	0.000	0.001
deepblue_faceting_experiments	0.092	0.000	0.454
deepblue_filter_regions	0.020	0.000	0.656
deepblue_flank	0.040	0.004	1.050
deepblue_get_biosource_children	0.012	0.008	0.372
deepblue_get_biosource_parents	0.016	0.000	0.372
deepblue_get_biosource_related	0.020	0.000	0.402
deepblue_get_biosource_synonyms	0.016	0.000	0.364
deepblue_get_experiments_by_query	0.016	0.000	0.374
deepblue_get_regions	0.040	0.000	0.974
deepblue_get_request_data	0.060	0.000	1.715
deepblue_info	0.072	0.000	0.426
deepblue_input_regions	0.016	0.000	0.560
deepblue_intersection	0.060	0.000	1.739
deepblue_is_biosource	0.016	0.000	0.367
deepblue_list_annotations	0.036	0.004	0.388
deepblue_list_biosources	0.016	0.000	0.363
deepblue_list_column_types	0.104	0.008	0.628
deepblue_list_epigenetic_marks	0.704	0.004	1.633
deepblue_list_experiments	0.096	0.000	0.453
deepblue_list_gene_expressions	0.024	0.000	0.375
deepblue_list_gene_models	0.016	0.000	0.368
deepblue_list_genes	0.116	0.000	0.932
deepblue_list_genomes	0.020	0.000	0.364
deepblue_list_in_use	0.772	0.008	2.217
deepblue_list_projects	0.016	0.000	0.386
deepblue_list_recent_experiments	0.020	0.008	0.379
deepblue_list_requests	0.016	0.000	0.519
deepblue_list_samples	0.196	0.000	0.909
deepblue_list_similar_biosources	0.04	0.00	0.60
deepblue_list_similar_epigenetic_marks	0.036	0.000	0.390
deepblue_list_similar_experiments	0.020	0.000	2.441
deepblue_list_similar_genomes	0.016	0.000	0.361
deepblue_list_similar_projects	0.016	0.000	0.385
deepblue_list_similar_techniques	0.020	0.000	0.363
deepblue_list_techniques	0.040	0.000	0.391
deepblue_merge_queries	0.060	0.000	1.569
deepblue_name_to_id	0.052	0.000	1.121
deepblue_preview_experiment	0.016	0.000	0.372
deepblue_query_cache	0.072	0.000	1.959
deepblue_query_experiment_type	0.036	0.008	0.890
deepblue_score_matrix	0.040	0.004	0.885
deepblue_search	0.080	0.004	0.664
deepblue_select_annotations	0.024	0.000	0.510
deepblue_select_experiments	0.020	0.000	0.518
deepblue_select_gene_expressions	0.024	0.000	0.697
deepblue_select_genes	0.024	0.000	0.666
deepblue_select_regions	0.028	0.000	0.507
deepblue_tiling_regions	0.016	0.000	0.500