BioC 3.3: CHECK report for SpidermiR on oaxaca

Package: SpidermiR

Version: 1.2.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpidermiR_1.2.5.tar.gz

StartedAt: 2016-10-13 06:34:15 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:42:19 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 484.0 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_1.2.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SpidermiR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.2.5’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 47.7Mb
  sub-directories of 1Mb or more:
    data  44.7Mb
    doc    2.9Mb
* 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 ... NOTE
SpidermiRvisualize_plot_target: no visible binding for global variable
  ‘miRNAs’
SpidermiRvisualize_plot_target: no visible binding for global variable
  ‘mRNA_target’
Undefined global functions or variables:
  mRNA_target miRNAs
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
SpidermiRdownload_miRNAprediction    10.103  1.394  28.091
SpidermiRanalyze_mirna_network        4.967  0.667   9.055
SpidermiRanalyze_mirna_gene_complnet  4.639  0.589   8.558
SpidermiRanalyze_DEnetworkTCGA        4.794  0.402   5.200
SpidermiRdownload_miRNAvalidate       4.051  0.505   5.964
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/SpidermiR.Rcheck/00check.log’
for details.

* installing *source* package ‘SpidermiR’ ...
** R
** data
*** moving datasets to lazyload DB
** 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	0.000	0.017
SpidermiRanalyze_Community_detection_bi	0.019	0.000	0.020
SpidermiRanalyze_Community_detection_net	0.016	0.000	0.017
SpidermiRanalyze_DEnetworkTCGA	4.794	0.402	5.200
SpidermiRanalyze_degree_centrality	0.003	0.000	0.002
SpidermiRanalyze_direct_net	0.004	0.000	0.004
SpidermiRanalyze_direct_subnetwork	0.005	0.001	0.005
SpidermiRanalyze_mirna_extra_cir	0.438	0.030	3.332
SpidermiRanalyze_mirna_gene_complnet	4.639	0.589	8.558
SpidermiRanalyze_mirna_network	4.967	0.667	9.055
SpidermiRanalyze_mirnanet_pharm	0.001	0.000	0.002
SpidermiRanalyze_subnetwork_neigh	0.009	0.000	0.010
SpidermiRdownload_miRNAextra_cir	0.078	0.008	2.378
SpidermiRdownload_miRNAprediction	10.103	1.394	28.091
SpidermiRdownload_miRNAvalidate	4.051	0.505	5.964
SpidermiRdownload_net	0.268	0.017	2.401
SpidermiRdownload_pharmacomir	0.016	0.001	0.497
SpidermiRprepare_NET	0.512	0.054	2.458
SpidermiRquery_disease	0.028	0.004	1.755
SpidermiRquery_networks_type	0.015	0.001	0.482
SpidermiRquery_spec_networks	0.064	0.000	0.531
SpidermiRquery_species	0.012	0.000	0.232
SpidermiRvisualize_3Dbarplot	0.118	0.001	0.118
SpidermiRvisualize_BI	0.051	0.007	0.216
SpidermiRvisualize_adj_matrix	0.059	0.001	0.061
SpidermiRvisualize_degree_dist	0.013	0.002	0.017
SpidermiRvisualize_direction	0.037	0.015	0.134
SpidermiRvisualize_mirnanet	0.029	0.003	0.032
SpidermiRvisualize_plot_target	0.220	0.001	0.223