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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SurfR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SurfR_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SurfR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SurfR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SurfR’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SurfR’ 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 ‘SurfR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TCGA_download
> ### Title: TCGA_download function
> ### Aliases: TCGA_download
> 
> ### ** Examples
> 
> GBM_list_s1 <- TCGA_download(project="TCGA-GBM",
+                              whichcounts = "unstranded",
+                              save.matrix = FALSE, save.metadata = FALSE,
+                              barcodes = c("TCGA-06-0878-01A-01R-1849-01"))
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-GBM
--------------------
oo Filtering results
--------------------
ooo By data.type
ooo By workflow.type
ooo By barcode
ooo By sample.type
----------------
oo Checking data
----------------
ooo Checking if there are duplicated cases
ooo Checking if there are results for the query
-------------------
o Preparing output
-------------------
Downloading data for project TCGA-GBM
trying URL '/system/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip'
Warning in download.file(url, ...) :
  URL '/system/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip': status was 'URL using bad/illegal format or missing URL'
Downloading data for project TCGA-GBM
GDCdownload will download: 4.221558 MB
Downloading as: 209797f2-6e12-4f02-bea7-fd559305fad4.rna_seq.augmented_star_gene_counts.tsv

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
File corrupted:209797f2-6e12-4f02-bea7-fd559305fad4.rna_seq.augmented_star_gene_counts.tsv
Run GDCdownload again to download it
Error in GDCprepare(query, summarizedExperiment = TRUE) : 
  I couldn't find all the files from the query. Please check if the directory parameter is right or `GDCdownload` downloaded the samples.
Calls: TCGA_download -> GDCprepare
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SurfR.Rcheck/00check.log’
for details.