BioC 3.3: CHECK report for SpidermiR on morelia

Package: SpidermiR

Version: 0.99.17

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpidermiR_0.99.17.tar.gz

StartedAt: 2016-04-21 07:48:48 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:49:41 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 52.6 seconds

RetCode: 0

Status:  OK

CheckDir: SpidermiR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpidermiR_0.99.17.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SpidermiR.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpidermiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpidermiR’ version ‘0.99.17’
* 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 ‘SpidermiR’ can be installed ... [1s/2s] 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 ... [13s/26s] OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
SpidermiRanalyze_mirna_gene_complnet 5.731  0.696   8.477
SpidermiRanalyze_mirna_network       4.236  0.577   7.408
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [1s/3s]
 [1s/3s] 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 ‘SpidermiR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SpidermiR)

name	user	system	elapsed
SpidermiRanalyze_Community_detection	0.016	0.001	0.016
SpidermiRanalyze_Community_detection_bi	0.017	0.000	0.018
SpidermiRanalyze_Community_detection_net	0.014	0.000	0.015
SpidermiRanalyze_degree_centrality	0.002	0.000	0.002
SpidermiRanalyze_direct_net	0.004	0.001	0.004
SpidermiRanalyze_direct_subnetwork	0.005	0.000	0.006
SpidermiRanalyze_mirna_extra_cir	0.410	0.010	2.762
SpidermiRanalyze_mirna_gene_complnet	5.731	0.696	8.477
SpidermiRanalyze_mirna_network	4.236	0.577	7.408
SpidermiRanalyze_mirnanet_pharm	0.003	0.000	0.002
SpidermiRanalyze_subnetwork_neigh	0.008	0.001	0.009
SpidermiRdownload_net	0.199	0.016	1.423
SpidermiRdownload_pharmacomir	0.014	0.001	0.454
SpidermiRprepare_NET	0.598	0.058	2.138
SpidermiRquery_disease	0.026	0.005	0.809
SpidermiRquery_networks_type	0.016	0.001	0.627
SpidermiRquery_spec_networks	0.059	0.000	0.356
SpidermiRquery_species	0.011	0.001	0.211
SpidermiRvisualize_BI	0.049	0.006	0.105
SpidermiRvisualize_mirnanet	0.031	0.004	0.034