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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RTCGAToolbox.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RTCGAToolbox_2.26.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RTCGAToolbox.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 ‘RTCGAToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTCGAToolbox’ version ‘2.26.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RTCGAToolbox’ 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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘RTCGAToolbox-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getBroadSubtypes
> ### Title: Download expression-based cancer subtypes from the Broad
> ###   Institute
> ### Aliases: getBroadSubtypes
> 
> ### ** Examples
> 
> co <- getBroadSubtypes("COAD", "CNMF")
Warning in getBroadSubtypes("COAD", "CNMF") :
  mRNA clustering not available for COAD - mRNAseq clustering is taken instead
Warning in file(file, "rt") :
  cannot open URL 'http://gdac.broadinstitute.org/runs/analyses__latest/reports/cancer/COAD-TP/mRNAseq_Clustering_CNMF/COAD-TP.bestclus.txt': HTTP status was '504 Gateway Timeout'
Error in file(file, "rt") : 
  cannot open the connection to 'http://gdac.broadinstitute.org/runs/analyses__latest/reports/cancer/COAD-TP/mRNAseq_Clustering_CNMF/COAD-TP.bestclus.txt'
Calls: getBroadSubtypes -> read.delim -> read.table -> 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
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/RTCGAToolbox.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL RTCGAToolbox
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘RTCGAToolbox’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** 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 (RTCGAToolbox)