Multiple platform build/check report for BioC 3.10 - CHECK report for SpidermiR on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SpidermiR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SpidermiR_1.16.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/SpidermiR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.16.2’
* 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 ... WARNING
Found the following significant warnings:
  Note: possible error in 'simpleNetwork(NetworkData, ': unused argument (textColour = "black") 
See ‘/home/biocbuild/bbs-3.10-bioc/meat/SpidermiR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘TCGAbiolinks’
  All declared Imports should be used.
* 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")
SpidermiRdownload_pharmacomir: no visible binding for global variable
  ‘drug_gene’
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:
  drug_gene 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
SpidermiRdownload_miRNAvalidate       8.112  0.296  12.932
SpidermiRdownload_pharmacomir         7.540  0.424  13.015
SpidermiRdownload_miRNAprediction     5.868  0.948  34.302
SpidermiRdownload_miRNAprediction_mmu 3.684  0.500  21.768
SpidermiRquery_disease                0.944  0.028  15.909
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/SpidermiR.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SpidermiR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘SpidermiR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'simpleNetwork(NetworkData, ': unused argument (textColour = "black") 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpidermiR)

Tests output

Example timings

name	user	system	elapsed
SpidermiRanalyze_Community_detection	0.012	0.000	0.011
SpidermiRanalyze_Community_detection_bi	0.184	0.012	0.197
SpidermiRanalyze_Community_detection_net	0.004	0.000	0.006
SpidermiRanalyze_degree_centrality	0.004	0.000	0.001
SpidermiRanalyze_direct_net	0.000	0.000	0.002
SpidermiRanalyze_direct_subnetwork	0.004	0.000	0.003
SpidermiRanalyze_subnetwork_neigh	0.004	0.000	0.004
SpidermiRdownload_drug_gene	0.464	0.032	1.550
SpidermiRdownload_miRNAextra_cir	0.132	0.000	1.288
SpidermiRdownload_miRNAprediction	5.868	0.948	34.302
SpidermiRdownload_miRNAprediction_mmu	3.684	0.500	21.768
SpidermiRdownload_miRNAvalidate	8.112	0.296	12.932
SpidermiRdownload_net	0.292	0.020	1.560
SpidermiRdownload_pharmacomir	7.540	0.424	13.015
SpidermiRprepare_NET	0.804	0.016	1.828
SpidermiRquery_disease	0.944	0.028	15.909
SpidermiRquery_networks_type	0.024	0.000	0.460
SpidermiRquery_spec_networks	0.084	0.000	0.329
SpidermiRquery_species	0.012	0.004	0.192
SpidermiRvisualize_3Dbarplot	0.120	0.012	0.138
SpidermiRvisualize_BI	0.132	0.012	0.165
SpidermiRvisualize_adj_matrix	0.056	0.000	0.059
SpidermiRvisualize_degree_dist	0.012	0.000	0.009
SpidermiRvisualize_direction	0.024	0.000	0.026
SpidermiRvisualize_mirnanet	0.016	0.004	0.020
SpidermiRvisualize_plot_target	0.180	0.000	0.182

CHECK report for SpidermiR on malbec1

Summary

Command output

Installation output

Tests output

Example timings