BioC 3.5: CHECK report for SpidermiR on veracruz2

Package: SpidermiR

Version: 1.7.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpidermiR_1.7.4.tar.gz

StartedAt: 2017-10-18 09:19:21 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:25:46 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 385.2 seconds

RetCode: 0

Status:  OK

CheckDir: SpidermiR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpidermiR_1.7.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SpidermiR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.7.4’
* 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      7.133  0.383  13.780
SpidermiRdownload_miRNAprediction    4.739  1.234  10.543
SpidermiRanalyze_mirna_gene_complnet 3.230  0.193   5.503
* 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	0.000	0.000	0.001
Case_Study1_loading_2_network	0.001	0.000	0.000
Case_Study1_loading_3_network	0	0	0
Case_Study1_loading_4_network	0.001	0.000	0.000
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	0.060	0.002	0.065
SpidermiRanalyze_Community_detection_bi	0.395	0.004	0.412
SpidermiRanalyze_Community_detection_net	0.008	0.000	0.009
SpidermiRanalyze_DEnetworkTCGA	2.832	0.077	2.997
SpidermiRanalyze_degree_centrality	0.003	0.001	0.003
SpidermiRanalyze_direct_net	0.042	0.000	0.043
SpidermiRanalyze_direct_subnetwork	0.045	0.001	0.046
SpidermiRanalyze_mirna_gene_complnet	3.230	0.193	5.503
SpidermiRanalyze_mirna_network	2.874	0.177	4.832
SpidermiRanalyze_mirnanet_pharm	0.001	0.000	0.001
SpidermiRanalyze_subnetwork_neigh	0.003	0.000	0.003
SpidermiRdownload_miRNALNC_RNA	0.121	0.008	4.383
SpidermiRdownload_miRNALNC_miRNA	0.049	0.003	2.264
SpidermiRdownload_miRNAextra_cir	0.063	0.006	1.749
SpidermiRdownload_miRNAprediction	4.739	1.234	10.543
SpidermiRdownload_miRNAvalidate	7.133	0.383	13.780
SpidermiRdownload_net	0.473	0.017	1.408
SpidermiRdownload_pharmacomir	0.013	0.001	0.335
SpidermiRprepare_NET	0.500	0.037	1.670
SpidermiRquery_disease	0.027	0.003	0.476
SpidermiRquery_networks_type	0.015	0.001	0.334
SpidermiRquery_spec_networks	0.050	0.001	0.231
SpidermiRquery_species	0.008	0.000	0.122
SpidermiRvisualize_3Dbarplot	0.114	0.001	0.117
SpidermiRvisualize_BI	0.216	0.005	0.232
SpidermiRvisualize_adj_matrix	0.063	0.002	0.065
SpidermiRvisualize_degree_dist	0.009	0.001	0.010
SpidermiRvisualize_direction	0.186	0.009	0.210
SpidermiRvisualize_mirnanet	0.062	0.003	0.071
SpidermiRvisualize_plot_target	1.068	0.007	1.103