##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CVE.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CVE_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CVE.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CVE/DESCRIPTION' ... OK
* this is package 'CVE' version '1.14.0'
* package encoding: UTF-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 whether package 'CVE' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'CVE' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CVE.Rcheck/00install.out' for details.
* 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: 'RTCGAToolbox'
  All declared Imports should be used.
Package in Depends field not imported from: 'tidyverse'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                old_size new_size compress
  WGCNAmelanoma_extension.RData    2.4Mb    2.1Mb       xz
  crcCase.RData                    1.1Mb    677Kb       xz
  melanomaCase.RData               654Kb    473Kb       xz
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'CVE-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get.oncotator.anno
> ### Title: Open Cancer Variant Explorer (CVE) Shiny app
> ### Aliases: get.oncotator.anno
> 
> ### ** Examples
> 
> exCase <- data.frame(chr = rep(10, 3),
+     start = c("100894110", "100985376", "101137905"),
+     end = c("100894110", "100985376", "101137905"),
+     ref_allele = c("T", "C", "G"),
+     obs_allele = c("G", "A", "A"))
> get.oncotator.anno(exCase)
Error in open.connection(con, "rb") : HTTP error 502.
Calls: get.oncotator.anno ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'CVE-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get.oncotator.anno
> ### Title: Open Cancer Variant Explorer (CVE) Shiny app
> ### Aliases: get.oncotator.anno
> 
> ### ** Examples
> 
> exCase <- data.frame(chr = rep(10, 3),
+     start = c("100894110", "100985376", "101137905"),
+     end = c("100894110", "100985376", "101137905"),
+     ref_allele = c("T", "C", "G"),
+     obs_allele = c("G", "A", "A"))
> get.oncotator.anno(exCase)
Error in open.connection(con, "rb") : HTTP error 502.
Calls: get.oncotator.anno ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
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, 2 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/CVE.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CVE_1.14.0.tar.gz && rm -rf CVE.buildbin-libdir && mkdir CVE.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CVE.buildbin-libdir CVE_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CVE_1.14.0.zip && rm CVE_1.14.0.tar.gz CVE_1.14.0.zip
###
##############################################################################
##############################################################################


  % 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 4218k  100 4218k    0     0  19.6M      0 --:--:-- --:--:-- --:--:-- 20.1M

install for i386

* installing *source* package 'CVE' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CVE'
    finding HTML links ... done
    GS_UV                                   html  
    GS_Vem                                  html  
    GS_lscore                               html  
    GS_pmet                                 html  
    GS_survival                             html  
    METree_GO                               html  
    MM                                      html  
    MS_UV                                   html  
    MS_UV_bar                               html  
    MS_Vem_bar                              html  
    MS_lscore                               html  
    MS_lscore_bar                           html  
    MS_pmet                                 html  
    MS_pmet_bar                             html  
    MS_survival                             html  
    MS_survival_bar                         html  
    MS_vem                                  html  
    crcCase                                 html  
    genes_WGCNA                             html  
    get.oncotator.anno                      html  
    label_order                             html  
    melanomaCase                            html  
    modules                                 html  
    openCVE                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'CVE' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'CVE' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CVE' ...
** testing if installed package can be loaded
Warning: Package 'CVE' is deprecated and will be removed from Bioconductor
  version 3.12
* MD5 sums
packaged installation of 'CVE' as CVE_1.14.0.zip
* DONE (CVE)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CVE' successfully unpacked and MD5 sums checked