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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpidermiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SpidermiR_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SpidermiR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'SpidermiR' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'simpleNetwork(NetworkData, ': unused argument (textColour = "black") 
See 'C:/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... 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(entrezfile, tmpfile, quiet = TRUE) :
  InternetOpenUrl failed: ''
Error in download.file(entrezfile, tmpfile, quiet = TRUE) : 
  cannot open URL 'ftp://ftp.ensembl.org/pub/release-HREF="/pub/99/"><B>99</B></A>/tsv/mus_musculus/Mus_musculus.GRCm38.HREF="/pub/99/"><B>99</B></A>.entrez.tsv.gz'
Calls: SpidermiRdownload_miRNAprediction_mmu -> TransGeneID -> getGeneAnn -> download.file
Execution halted
** running examples for arch 'x64' ... 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(entrezfile, tmpfile, quiet = TRUE) :
  InternetOpenUrl failed: ''
Error in download.file(entrezfile, tmpfile, quiet = TRUE) : 
  cannot open URL 'ftp://ftp.ensembl.org/pub/release-HREF="/pub/99/"><B>99</B></A>/tsv/mus_musculus/Mus_musculus.GRCm38.HREF="/pub/99/"><B>99</B></A>.entrez.tsv.gz'
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: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/SpidermiR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SpidermiR_1.20.0.tar.gz && rm -rf SpidermiR.buildbin-libdir && mkdir SpidermiR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpidermiR.buildbin-libdir SpidermiR_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SpidermiR_1.20.0.zip && rm SpidermiR_1.20.0.tar.gz SpidermiR_1.20.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100 22594  100 22594    0     0  1184k      0 --:--:-- --:--:-- --:--:-- 1225k

install for i386

* 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
  converting help for package 'SpidermiR'
    finding HTML links ... done
    SpidermiRanalyze_Community_detection    html  
    SpidermiRanalyze_Community_detection_bi
                                            html  
    SpidermiRanalyze_Community_detection_net
                                            html  
    SpidermiRanalyze_degree_centrality      html  
    SpidermiRanalyze_direct_net             html  
    SpidermiRanalyze_direct_subnetwork      html  
    SpidermiRanalyze_subnetwork_neigh       html  
    SpidermiRdownload_drug_gene             html  
    SpidermiRdownload_miRNAextra_cir        html  
    SpidermiRdownload_miRNAprediction       html  
    SpidermiRdownload_miRNAprediction_mmu   html  
    SpidermiRdownload_miRNAvalidate         html  
    SpidermiRdownload_net                   html  
    SpidermiRdownload_pharmacomir           html  
    SpidermiRprepare_NET                    html  
    SpidermiRquery_disease                  html  
    SpidermiRquery_networks_type            html  
    SpidermiRquery_spec_networks            html  
    SpidermiRquery_species                  html  
    SpidermiRvisualize_3Dbarplot            html  
    SpidermiRvisualize_BI                   html  
    SpidermiRvisualize_adj_matrix           html  
    SpidermiRvisualize_degree_dist          html  
    SpidermiRvisualize_direction            html  
    SpidermiRvisualize_mirnanet             html  
    SpidermiRvisualize_plot_target          html  
** 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

install for x64

* installing *source* package 'SpidermiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpidermiR' as SpidermiR_1.20.0.zip
* DONE (SpidermiR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SpidermiR' successfully unpacked and MD5 sums checked