BioC 3.4: CHECK report for SpidermiR on morelia

Package: SpidermiR

Version: 1.4.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpidermiR_1.4.8.tar.gz

StartedAt: 2017-04-15 08:25:17 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:33:06 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 469.0 seconds

RetCode: 0

Status:  OK

CheckDir: SpidermiR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpidermiR_1.4.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SpidermiR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.8’
* 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 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    9.171  1.890  41.241
SpidermiRanalyze_mirna_gene_complnet 7.954  0.525  10.696
SpidermiRanalyze_mirna_network       5.020  0.428   7.799
SpidermiRdownload_miRNAvalidate      3.983  0.437   5.769
* 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-3.4-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	0.001	0.000	0.001
Case_Study1_loading_2_network	0	0	0
Case_Study1_loading_3_network	0.001	0.000	0.000
Case_Study1_loading_4_network	0	0	0
Case_Study2_loading_1_network	0.001	0.000	0.001
Case_Study2_loading_2_network	0.000	0.000	0.001
Case_Study2_loading_3_network	0.001	0.000	0.001
SpidermiRanalyze_Community_detection	0.021	0.001	0.022
SpidermiRanalyze_Community_detection_bi	0.026	0.001	0.027
SpidermiRanalyze_Community_detection_net	0.018	0.001	0.019
SpidermiRanalyze_DEnetworkTCGA	2.776	0.099	2.878
SpidermiRanalyze_degree_centrality	0.003	0.000	0.003
SpidermiRanalyze_direct_net	0.004	0.000	0.004
SpidermiRanalyze_direct_subnetwork	0.006	0.001	0.006
SpidermiRanalyze_mirna_gene_complnet	7.954	0.525	10.696
SpidermiRanalyze_mirna_network	5.020	0.428	7.799
SpidermiRanalyze_mirnanet_pharm	0.000	0.000	0.001
SpidermiRanalyze_subnetwork_neigh	0.008	0.000	0.009
SpidermiRdownload_miRNAextra_cir	0.067	0.006	4.237
SpidermiRdownload_miRNAprediction	9.171	1.890	41.241
SpidermiRdownload_miRNAvalidate	3.983	0.437	5.769
SpidermiRdownload_net	0.205	0.016	1.579
SpidermiRdownload_pharmacomir	0.001	0.000	0.000
SpidermiRprepare_NET	0.543	0.049	2.253
SpidermiRquery_disease	0.028	0.004	2.358
SpidermiRquery_networks_type	0.017	0.001	0.514
SpidermiRquery_spec_networks	0.053	0.001	0.547
SpidermiRquery_species	0.013	0.000	0.349
SpidermiRvisualize_3Dbarplot	0.148	0.001	0.149
SpidermiRvisualize_BI	0.057	0.007	0.140
SpidermiRvisualize_adj_matrix	0.065	0.001	0.066
SpidermiRvisualize_degree_dist	0.010	0.001	0.012
SpidermiRvisualize_direction	0.032	0.013	0.331
SpidermiRvisualize_mirnanet	0.038	0.004	0.041
SpidermiRvisualize_plot_target	0.276	0.002	0.279