BioC 3.5: CHECK report for SpidermiR on oaxaca

Package: SpidermiR

Version: 1.5.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpidermiR_1.5.6.tar.gz

StartedAt: 2017-03-04 09:29:50 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:38:22 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 511.8 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_1.5.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SpidermiR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.5.6’
* 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 ... 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 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    10.551  1.931  35.249
SpidermiRanalyze_mirna_gene_complnet  3.814  0.279   6.148
SpidermiRanalyze_mirna_network        2.959  0.224   5.213
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-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
Case_Study1_loading_1_network	0.001	0.000	0.000
Case_Study1_loading_2_network	0.000	0.000	0.001
Case_Study1_loading_3_network	0.001	0.000	0.000
Case_Study1_loading_4_network	0.001	0.000	0.001
Case_Study2_loading_1_network	0.000	0.000	0.001
Case_Study2_loading_2_network	0	0	0
Case_Study2_loading_3_network	0.000	0.000	0.001
SpidermiRanalyze_Community_detection	0.111	0.001	0.112
SpidermiRanalyze_Community_detection_bi	1.119	0.003	1.125
SpidermiRanalyze_Community_detection_net	0.014	0.000	0.014
SpidermiRanalyze_DEnetworkTCGA	3.081	0.105	3.188
SpidermiRanalyze_degree_centrality	0.003	0.000	0.003
SpidermiRanalyze_direct_net	0.050	0.001	0.050
SpidermiRanalyze_direct_subnetwork	0.061	0.000	0.061
SpidermiRanalyze_mirna_extra_cir	0.454	0.013	2.640
SpidermiRanalyze_mirna_gene_complnet	3.814	0.279	6.148
SpidermiRanalyze_mirna_network	2.959	0.224	5.213
SpidermiRanalyze_mirnanet_pharm	0.002	0.000	0.003
SpidermiRanalyze_subnetwork_neigh	0.010	0.001	0.010
SpidermiRdownload_miRNAextra_cir	0.081	0.007	2.267
SpidermiRdownload_miRNAprediction	10.551	1.931	35.249
SpidermiRdownload_miRNAvalidate	3.198	0.310	4.878
SpidermiRdownload_net	0.543	0.017	2.018
SpidermiRdownload_pharmacomir	0.016	0.001	1.277
SpidermiRprepare_NET	0.668	0.055	2.403
SpidermiRquery_disease	0.027	0.003	0.796
SpidermiRquery_networks_type	0.016	0.001	0.820
SpidermiRquery_spec_networks	0.061	0.000	0.566
SpidermiRquery_species	0.009	0.001	0.339
SpidermiRvisualize_3Dbarplot	0.130	0.002	0.133
SpidermiRvisualize_BI	0.333	0.009	0.415
SpidermiRvisualize_adj_matrix	0.090	0.003	0.094
SpidermiRvisualize_degree_dist	0.017	0.001	0.020
SpidermiRvisualize_direction	0.259	0.014	0.323
SpidermiRvisualize_mirnanet	0.091	0.006	0.098
SpidermiRvisualize_plot_target	1.359	0.027	1.387