BioC 3.5: CHECK report for SpidermiR on malbec2

Package: SpidermiR

Version: 1.7.4

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SpidermiR_1.7.4.tar.gz

StartedAt: 2017-10-18 02:39:04 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:44:39 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 334.1 seconds

RetCode: 0

Status:  OK

CheckDir: SpidermiR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SpidermiR_1.7.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/SpidermiR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.7.4’
* 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 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      5.456  0.200  12.798
SpidermiRdownload_miRNAprediction    4.236  0.652  19.314
SpidermiRanalyze_mirna_gene_complnet 2.884  0.020   5.102
SpidermiRdownload_miRNALNC_RNA       0.212  0.004   6.691
* 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-3.5-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	0.004	0.000	0.000
Case_Study1_loading_2_network	0	0	0
Case_Study1_loading_3_network	0	0	0
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	0.040	0.004	0.045
SpidermiRanalyze_Community_detection_bi	0.292	0.008	0.300
SpidermiRanalyze_Community_detection_net	0.008	0.000	0.006
SpidermiRanalyze_DEnetworkTCGA	4.200	0.016	4.216
SpidermiRanalyze_degree_centrality	0.004	0.000	0.002
SpidermiRanalyze_direct_net	0.028	0.000	0.028
SpidermiRanalyze_direct_subnetwork	0.036	0.000	0.034
SpidermiRanalyze_mirna_gene_complnet	2.884	0.020	5.102
SpidermiRanalyze_mirna_network	2.232	0.016	4.312
SpidermiRanalyze_mirnanet_pharm	0.000	0.000	0.001
SpidermiRanalyze_subnetwork_neigh	0.004	0.000	0.004
SpidermiRdownload_miRNALNC_RNA	0.212	0.004	6.691
SpidermiRdownload_miRNALNC_miRNA	0.064	0.000	4.253
SpidermiRdownload_miRNAextra_cir	0.096	0.004	1.412
SpidermiRdownload_miRNAprediction	4.236	0.652	19.314
SpidermiRdownload_miRNAvalidate	5.456	0.200	12.798
SpidermiRdownload_net	0.496	0.020	1.250
SpidermiRdownload_pharmacomir	0.012	0.004	0.353
SpidermiRprepare_NET	0.660	0.020	1.581
SpidermiRquery_disease	0.040	0.004	0.645
SpidermiRquery_networks_type	0.028	0.000	0.316
SpidermiRquery_spec_networks	0.084	0.000	0.357
SpidermiRquery_species	0.020	0.000	0.126
SpidermiRvisualize_3Dbarplot	0.164	0.000	0.163
SpidermiRvisualize_BI	0.228	0.004	0.275
SpidermiRvisualize_adj_matrix	0.060	0.000	0.061
SpidermiRvisualize_degree_dist	0.012	0.000	0.010
SpidermiRvisualize_direction	0.216	0.012	0.260
SpidermiRvisualize_mirnanet	0.080	0.008	0.089
SpidermiRvisualize_plot_target	0.812	0.004	0.819