BioC 3.3: CHECK report for SpidermiR on zin2

Package: SpidermiR

Version: 1.2.5

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SpidermiR_1.2.5.tar.gz

StartedAt: 2016-10-13 07:04:38 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:10:55 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 376.5 seconds

RetCode: 0

Status:  OK

CheckDir: SpidermiR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SpidermiR_1.2.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.2.5’
* 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 ... NOTE
  installed size is 47.3Mb
  sub-directories of 1Mb or more:
    data  44.7Mb
    doc    2.5Mb
* 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 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_miRNAprediction    8.590  0.285  16.866
SpidermiRanalyze_DEnetworkTCGA       6.077  0.148   6.242
SpidermiRanalyze_mirna_gene_complnet 4.145  0.108   7.511
SpidermiRanalyze_mirna_network       3.787  0.020   7.178
SpidermiRdownload_miRNAvalidate      3.533  0.004   5.263
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-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
SpidermiRanalyze_Community_detection	0.012	0.000	0.012
SpidermiRanalyze_Community_detection_bi	0.013	0.000	0.014
SpidermiRanalyze_Community_detection_net	0.012	0.000	0.011
SpidermiRanalyze_DEnetworkTCGA	6.077	0.148	6.242
SpidermiRanalyze_degree_centrality	0.002	0.000	0.003
SpidermiRanalyze_direct_net	0.002	0.000	0.003
SpidermiRanalyze_direct_subnetwork	0.004	0.000	0.003
SpidermiRanalyze_mirna_extra_cir	0.323	0.000	2.636
SpidermiRanalyze_mirna_gene_complnet	4.145	0.108	7.511
SpidermiRanalyze_mirna_network	3.787	0.020	7.178
SpidermiRanalyze_mirnanet_pharm	0.002	0.000	0.002
SpidermiRanalyze_subnetwork_neigh	0.003	0.004	0.007
SpidermiRdownload_miRNAextra_cir	0.062	0.005	1.634
SpidermiRdownload_miRNAprediction	8.590	0.285	16.866
SpidermiRdownload_miRNAvalidate	3.533	0.004	5.263
SpidermiRdownload_net	0.174	0.000	1.481
SpidermiRdownload_pharmacomir	0.012	0.000	0.498
SpidermiRprepare_NET	0.437	0.008	3.474
SpidermiRquery_disease	0.027	0.000	1.431
SpidermiRquery_networks_type	0.018	0.000	0.611
SpidermiRquery_spec_networks	0.056	0.000	0.335
SpidermiRquery_species	0.013	0.000	0.201
SpidermiRvisualize_3Dbarplot	0.083	0.000	0.083
SpidermiRvisualize_BI	0.042	0.000	0.075
SpidermiRvisualize_adj_matrix	0.052	0.000	0.052
SpidermiRvisualize_degree_dist	0.012	0.000	0.011
SpidermiRvisualize_direction	0.027	0.008	0.080
SpidermiRvisualize_mirnanet	0.028	0.000	0.027
SpidermiRvisualize_plot_target	0.172	0.000	0.172