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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:RTCGAToolbox.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RTCGAToolbox_2.39.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RTCGAToolbox.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCGAToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTCGAToolbox’ version ‘2.39.1’
* 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 code 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 loading without being on the library search path ... 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 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: makeSummarizedExperimentFromGISTIC
> ### Title: Create a SummarizedExperiment from FireHose GISTIC
> ### Aliases: makeSummarizedExperimentFromGISTIC
> 
> ### ** Examples
> 
> 
> co <- getFirehoseData("COAD", clinical = FALSE, GISTIC = TRUE,
+     destdir = tempdir())
trying URL 'https://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/COAD-TP/20160128/gdac.broadinstitute.org_COAD-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 31302857 bytes (29.9 MB)
==========================
downloaded 15.9 MB

Warning in download.file(url = download_link, destfile = fileLoc, method = "auto",  :
  downloaded length 16639961 != reported length 31302857
Warning in download.file(url = download_link, destfile = fileLoc, method = "auto",  :
  URL 'https://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/COAD-TP/20160128/gdac.broadinstitute.org_COAD-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz': Timeout of 600 seconds was reached
Error in download.file(url = download_link, destfile = fileLoc, method = "auto",  : 
  download from 'https://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/COAD-TP/20160128/gdac.broadinstitute.org_COAD-TP.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz' failed
Calls: getFirehoseData -> download.file
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
biocExtract    7.303  0.259   7.584
getGISTICPeaks 5.114  0.197   8.248
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.22-bioc/meat/RTCGAToolbox.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL RTCGAToolbox
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘RTCGAToolbox’ ...
** this is package ‘RTCGAToolbox’ version ‘2.39.1’
** using staged installation
** R
** data
** 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)