BioC 3.4: CHECK report for SpidermiR on malbec1

Package: SpidermiR

Version: 1.4.8

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SpidermiR_1.4.8.tar.gz

StartedAt: 2017-04-15 01:25:22 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:31:01 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 338.8 seconds

RetCode: 0

Status:  OK

CheckDir: SpidermiR.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 SpidermiR_1.4.8.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SpidermiR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.8’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
SpidermiRanalyze_mirna_gene_complnet 7.608  0.072   8.896
SpidermiRdownload_miRNAprediction    6.308  0.228   6.538
SpidermiRanalyze_mirna_network       4.608  0.032   5.865
* 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
  ‘/home/biocbuild/bbs-3.4-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	0.000	0.000	0.001
Case_Study1_loading_2_network	0	0	0
Case_Study1_loading_3_network	0.004	0.000	0.000
Case_Study1_loading_4_network	0	0	0
Case_Study2_loading_1_network	0	0	0
Case_Study2_loading_2_network	0	0	0
Case_Study2_loading_3_network	0	0	0
SpidermiRanalyze_Community_detection	0.008	0.000	0.010
SpidermiRanalyze_Community_detection_bi	0.008	0.000	0.010
SpidermiRanalyze_Community_detection_net	0.008	0.000	0.009
SpidermiRanalyze_DEnetworkTCGA	4.400	0.012	4.419
SpidermiRanalyze_degree_centrality	0.000	0.000	0.002
SpidermiRanalyze_direct_net	0.004	0.000	0.002
SpidermiRanalyze_direct_subnetwork	0.000	0.004	0.003
SpidermiRanalyze_mirna_gene_complnet	7.608	0.072	8.896
SpidermiRanalyze_mirna_network	4.608	0.032	5.865
SpidermiRanalyze_mirnanet_pharm	0	0	0
SpidermiRanalyze_subnetwork_neigh	0.004	0.000	0.005
SpidermiRdownload_miRNAextra_cir	0.084	0.000	1.324
SpidermiRdownload_miRNAprediction	6.308	0.228	6.538
SpidermiRdownload_miRNAvalidate	3.324	0.012	4.360
SpidermiRdownload_net	0.324	0.000	1.110
SpidermiRdownload_pharmacomir	0	0	0
SpidermiRprepare_NET	0.728	0.016	1.468
SpidermiRquery_disease	0.036	0.000	0.251
SpidermiRquery_networks_type	0.024	0.000	0.402
SpidermiRquery_spec_networks	0.088	0.000	0.500
SpidermiRquery_species	0.020	0.000	0.316
SpidermiRvisualize_3Dbarplot	0.128	0.004	0.131
SpidermiRvisualize_BI	0.048	0.004	0.069
SpidermiRvisualize_adj_matrix	0.072	0.004	0.079
SpidermiRvisualize_degree_dist	0.016	0.000	0.016
SpidermiRvisualize_direction	0.036	0.012	0.116
SpidermiRvisualize_mirnanet	0.044	0.000	0.043
SpidermiRvisualize_plot_target	0.312	0.000	0.315