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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RTCGA.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RTCGA_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RTCGA.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCGA/DESCRIPTION’ ... OK
* this is package ‘RTCGA’ version ‘1.26.0’
* 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 ‘RTCGA’ 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
* 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
availableDates: no visible binding for global variable ‘.’
downloadTCGA: no visible binding for global variable ‘.’
ggbiplot: no visible binding for global variable ‘xvar’
ggbiplot: no visible binding for global variable ‘yvar’
ggbiplot: no visible global function definition for ‘muted’
ggbiplot: no visible binding for global variable ‘varname’
ggbiplot: no visible binding for global variable ‘angle’
ggbiplot: no visible binding for global variable ‘hjust’
read.mutations: no visible binding for global variable ‘.’
read.rnaseq: no visible binding for global variable ‘.’
survivalTCGA: no visible binding for global variable ‘times’
whichDateToUse: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . angle hjust muted times varname xvar yvar
* 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 ‘RTCGA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: checkTCGA
> ### Title: Information about datasets from TCGA project
> ### Aliases: checkTCGA
> 
> ### ** Examples
> 
> 
> ############################# 
> 
> # names for current release date and cohort
> checkTCGA('DataSets', 'BRCA' )
Warning in file(con, "r") :
  cannot open URL 'http://gdac.broadinstitute.org/runs/': HTTP status was '504 Gateway Timeout'
Error in file(con, "r") : 
  cannot open the connection to 'http://gdac.broadinstitute.org/runs/'
Calls: checkTCGA ... availableDates -> %>% -> assign -> readLines -> file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─RTCGA (local) expect_dimsSize_equal(list("ACC", "2015-06-01"), c(92, 1115)) at test_read.R:23:4
   2. │ └─RTCGA::downloadTCGA(...) at test_read.R:4:8
   3. │   └─RTCGA:::whichDateToUse(date = date)
   4. │     ├─date %in% availableDates()
   5. │     └─RTCGA:::availableDates()
   6. │       ├─readLines("http://gdac.broadinstitute.org/runs/") %>% ...
   7. │       └─base::readLines("http://gdac.broadinstitute.org/runs/")
   8. │         └─base::file(con, "r")
   9. └─base::assign(x = ".gdacContent", value = ., envir = .RTCGAEnv)
  
  [ FAIL 4 | WARN 3 | SKIP 0 | PASS 1 ]
  Error: Test failures
  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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/RTCGA.Rcheck/00check.log’
for details.