BioC 3.4: CHECK report for SpidermiR on zin1

Package: SpidermiR

Version: 1.2.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SpidermiR_1.2.2.tar.gz

StartedAt: 2016-09-20 12:52:32 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:01:34 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 541.6 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_1.2.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SpidermiR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.2.2’
* 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 loading without being on the library search path ... 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 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
SpidermiRanalyze_DEnetworkTCGA       184.640  7.280 220.229
SpidermiRdownload_miRNAprediction      7.476  0.312  12.597
SpidermiRanalyze_mirna_gene_complnet   6.476  0.112   9.090
SpidermiRanalyze_mirna_network         4.708  0.032   7.048
SpidermiRdownload_miRNAvalidate        3.556  0.120   5.227
* 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
** 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
SpidermiRanalyze_Community_detection	0.012	0.000	0.011
SpidermiRanalyze_Community_detection_bi	0.012	0.000	0.012
SpidermiRanalyze_Community_detection_net	0.012	0.000	0.011
SpidermiRanalyze_DEnetworkTCGA	184.640	7.280	220.229
SpidermiRanalyze_degree_centrality	0.004	0.000	0.002
SpidermiRanalyze_direct_net	0.000	0.000	0.003
SpidermiRanalyze_direct_subnetwork	0.000	0.000	0.003
SpidermiRanalyze_mirna_extra_cir	0.288	0.008	2.624
SpidermiRanalyze_mirna_gene_complnet	6.476	0.112	9.090
SpidermiRanalyze_mirna_network	4.708	0.032	7.048
SpidermiRanalyze_mirnanet_pharm	0.000	0.000	0.002
SpidermiRanalyze_subnetwork_neigh	0.008	0.000	0.006
SpidermiRdownload_miRNAextra_cir	0.064	0.000	1.821
SpidermiRdownload_miRNAprediction	7.476	0.312	12.597
SpidermiRdownload_miRNAvalidate	3.556	0.120	5.227
SpidermiRdownload_net	0.164	0.000	2.865
SpidermiRdownload_pharmacomir	0.008	0.000	0.634
SpidermiRprepare_NET	0.440	0.020	4.001
SpidermiRquery_disease	0.024	0.000	0.800
SpidermiRquery_networks_type	0.020	0.000	0.784
SpidermiRquery_spec_networks	0.056	0.000	0.535
SpidermiRquery_species	0.012	0.004	0.335
SpidermiRvisualize_3Dbarplot	0.084	0.000	0.084
SpidermiRvisualize_BI	0.040	0.004	0.055
SpidermiRvisualize_adj_matrix	0.052	0.000	0.054
SpidermiRvisualize_degree_dist	0.012	0.000	0.011
SpidermiRvisualize_direction	0.032	0.000	0.067
SpidermiRvisualize_mirnanet	0.028	0.000	0.028
SpidermiRvisualize_plot_target	0.168	0.000	0.169