BioC 3.5: CHECK report for SpidermiR on veracruz2

Package: SpidermiR

Version: 1.6.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpidermiR_1.6.3.tar.gz

StartedAt: 2017-08-16 08:29:49 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:35:53 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 364.1 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_1.6.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SpidermiR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.3’
* 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_gene: possible error in simpleNetwork(NetworkData,
  linkColour = "gray", textColour = "black", zoom = TRUE): unused
  argument (textColour = "black")
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_miRNAvalidate      7.810  0.372  13.636
SpidermiRdownload_miRNAprediction    4.235  1.138   9.286
SpidermiRanalyze_mirna_gene_complnet 3.252  0.183   5.745
* 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	0.000
Case_Study2_loading_1_network	0.001	0.000	0.001
Case_Study2_loading_2_network	0.001	0.000	0.001
Case_Study2_loading_3_network	0.001	0.000	0.000
SpidermiRanalyze_Community_detection	0.075	0.002	0.078
SpidermiRanalyze_Community_detection_bi	0.374	0.004	0.383
SpidermiRanalyze_Community_detection_net	0.008	0.000	0.008
SpidermiRanalyze_DEnetworkTCGA	3.313	0.078	3.478
SpidermiRanalyze_degree_centrality	0.003	0.000	0.003
SpidermiRanalyze_direct_net	0.027	0.001	0.032
SpidermiRanalyze_direct_subnetwork	0.048	0.000	0.050
SpidermiRanalyze_mirna_gene_complnet	3.252	0.183	5.745
SpidermiRanalyze_mirna_network	2.570	0.164	4.515
SpidermiRanalyze_mirnanet_pharm	0.001	0.000	0.002
SpidermiRanalyze_subnetwork_neigh	0.005	0.001	0.006
SpidermiRdownload_miRNAextra_cir	0.057	0.008	1.684
SpidermiRdownload_miRNAprediction	4.235	1.138	9.286
SpidermiRdownload_miRNAvalidate	7.810	0.372	13.636
SpidermiRdownload_net	0.403	0.014	1.645
SpidermiRdownload_pharmacomir	0.014	0.001	0.332
SpidermiRprepare_NET	0.566	0.050	1.996
SpidermiRquery_disease	0.029	0.003	0.505
SpidermiRquery_networks_type	0.016	0.001	0.503
SpidermiRquery_spec_networks	0.052	0.001	0.461
SpidermiRquery_species	0.008	0.000	0.277
SpidermiRvisualize_3Dbarplot	0.155	0.005	0.164
SpidermiRvisualize_BI	0.285	0.006	0.302
SpidermiRvisualize_adj_matrix	0.069	0.002	0.071
SpidermiRvisualize_degree_dist	0.012	0.001	0.013
SpidermiRvisualize_direction	0.231	0.011	0.247
SpidermiRvisualize_mirnanet	0.070	0.003	0.082
SpidermiRvisualize_plot_target	1.085	0.003	1.155