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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SpidermiR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SpidermiR_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/SpidermiR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.20.0’
* 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 ‘/Users/biocbuild/bbs-3.12-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 ... ERROR
Running examples in ‘SpidermiR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SpidermiRdownload_miRNAprediction_mmu
> ### Title: Download mmu miRNA predicted database
> ### Aliases: SpidermiRdownload_miRNAprediction_mmu
> 
> ### ** Examples
> 
> mirna<-c('mmu-miR-708-3p')
> list<-SpidermiRdownload_miRNAprediction_mmu(mirna_list=mirna)
[1] "Processing... mmu-miR-708-3p"
Loading required package: miRNAtap.db
[1] "Mapping to gene symbol mmu-miR-708-3p"
Warning in download.file(uniprot_link, locfname, quiet = TRUE) :
  URL 'https://www.uniprot.org/uniprot/?query=proteome:up000000589&format=tab&force=true&columns=id,entry%20name,reviewed,protein%20names,genes,organism,database(Ensembl),comment(SUBCELLULAR%20LOCATION),database(RefSeq),comment(ALTERNATIVE%20PRODUCTS)&sort=score': status was 'SSL connect error'
Error in download.file(uniprot_link, locfname, quiet = TRUE) : 
  cannot open URL 'https://www.uniprot.org/uniprot/?query=proteome:up000000589&format=tab&force=true&columns=id,entry%20name,reviewed,protein%20names,genes,organism,database(Ensembl),comment(SUBCELLULAR%20LOCATION),database(RefSeq),comment(ALTERNATIVE%20PRODUCTS)&sort=score'
Calls: SpidermiRdownload_miRNAprediction_mmu -> TransGeneID -> getGeneAnn -> download.file
Execution halted
* 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 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/SpidermiR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SpidermiR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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)