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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCANVIS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SCANVIS_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SCANVIS.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SCANVIS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SCANVIS' version '1.6.0'
* 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 'SCANVIS' 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SCANVISannotation: no visible global function definition for
  'download.file'
SCANVISannotation: no visible binding for global variable 'out.dir'
SCANVISannotation: no visible global function definition for
  'elementMetadata'
SCANVISannotation: no visible global function definition for 'seqnames'
SCANVISmerge: no visible global function definition for 'read.delim'
SCANVISread_STAR: no visible global function definition for
  'read.delim'
SCANVISscan: no visible global function definition for 'read.delim'
SCANVISscan: no visible global function definition for 'tail'
SCANVISscan: no visible global function definition for 'write.table'
SCANVISvisual: no visible global function definition for 'rect'
SCANVISvisual: no visible global function definition for 'lines'
SCANVISvisual: no visible global function definition for 'text'
SCANVISvisual: no visible global function definition for 'legend'
SCANVISvisual: no visible global function definition for 'write.table'
SCANVISvisual: no visible global function definition for 'read.delim'
SCANVISvisual: no visible global function definition for 'tail'
SCANVISvisual: no visible global function definition for 'head'
SCANVISvisual: no visible global function definition for 'points'
gene2roi: no visible global function definition for 'tail'
Undefined global functions or variables:
  download.file elementMetadata head legend lines out.dir points
  read.delim rect seqnames tail text write.table
Consider adding
  importFrom("graphics", "legend", "lines", "points", "rect", "text")
  importFrom("utils", "download.file", "head", "read.delim", "tail",
             "write.table")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'SCANVIS-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ls_url
> ### Title: list files available at annotation/gencode url
> ### Aliases: ls_url
> ### Keywords: gencode annotation GTF
> 
> ### ** Examples
> 
> ftpfiles=ls_url('ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/')
ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/
Error in ls_url("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/") : 
  url.exists(url) is not TRUE
Calls: ls_url -> stopifnot
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'SCANVIS-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ls_url
> ### Title: list files available at annotation/gencode url
> ### Aliases: ls_url
> ### Keywords: gencode annotation GTF
> 
> ### ** Examples
> 
> ftpfiles=ls_url('ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/')
ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/
Error in ls_url("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/") : 
  url.exists(url) is not TRUE
Calls: ls_url -> stopifnot
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 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/SCANVIS.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SCANVIS_1.6.0.tar.gz && rm -rf SCANVIS.buildbin-libdir && mkdir SCANVIS.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SCANVIS.buildbin-libdir SCANVIS_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SCANVIS_1.6.0.zip && rm SCANVIS_1.6.0.tar.gz SCANVIS_1.6.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  282k  100  282k    0     0  1056k      0 --:--:-- --:--:-- --:--:-- 1059k

install for i386

* installing *source* package 'SCANVIS' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SCANVIS'
    finding HTML links ... done
    GBM                                     html  
    IR2Mat                                  html  
    LUAD                                    html  
    LUSC                                    html  
    SCANVIS-package                         html  
    SCANVISannotation                       html  
    SCANVISexamples                         html  
    SCANVISlinkvar                          html  
    SCANVISmerge                            html  
    SCANVISreadSTAR                         html  
    SCANVISscan                             html  
    SCANVISvisual                           html  
    gbm3                                    html  
    gbm3.vcf                                html  
    gen19                                   html  
    gene2roi                                html  
    ls_url                                  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 'SCANVIS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SCANVIS' as SCANVIS_1.6.0.zip
* DONE (SCANVIS)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'SCANVIS' successfully unpacked and MD5 sums checked