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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GenomicDataCommons_1.23.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicDataCommons.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GenomicDataCommons/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicDataCommons’ version ‘1.23.2’
* 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 ‘GenomicDataCommons’ 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenomicDataCommons-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filtering
> ### Title: Manipulating GDCQuery filters
> ### Aliases: filtering filter filter.GDCQuery get_filter
> ###   get_filter.GDCQuery
> 
> ### ** Examples
> 
> # make a GDCQuery object to start
> #
> # Projects
> #
> pQuery = projects()
> 
> # check for the default fields
> # so that we can use one of them to build a filter
> default_fields(pQuery)
 [1] "dbgap_accession_number" "disease_type"           "intended_release_date" 
 [4] "name"                   "primary_site"           "project_autocomplete"  
 [7] "project_id"             "releasable"             "released"              
[10] "state"                 
> pQuery = filter(pQuery,~ project_id == 'TCGA-LUAC')
> get_filter(pQuery)
$op
[x] "="

$content
$content$field
[1] "project_id"

$content$value
[1] "TCGA-LUAC"


> 
> #
> # Files
> #
> fQuery = files()
> default_fields(fQuery)
 [1] "access"                         "acl"                           
 [3] "average_base_quality"           "average_insert_size"           
 [5] "average_read_length"            "channel"                       
 [7] "chip_id"                        "chip_position"                 
 [9] "contamination"                  "contamination_error"           
[11] "created_datetime"               "data_category"                 
[13] "data_format"                    "data_type"                     
[15] "error_type"                     "experimental_strategy"         
[17] "file_autocomplete"              "file_id"                       
[19] "file_name"                      "file_size"                     
[21] "imaging_date"                   "magnification"                 
[23] "md5sum"                         "mean_coverage"                 
[25] "msi_score"                      "msi_status"                    
[27] "pairs_on_diff_chr"              "plate_name"                    
[29] "plate_well"                     "platform"                      
[31] "proc_internal"                  "proportion_base_mismatch"      
[33] "proportion_coverage_10X"        "proportion_coverage_10x"       
[35] "proportion_coverage_30X"        "proportion_coverage_30x"       
[37] "proportion_reads_duplicated"    "proportion_reads_mapped"       
[39] "proportion_targets_no_coverage" "read_pair_number"              
[41] "revision"                       "stain_type"                    
[43] "state"                          "state_comment"                 
[45] "submitter_id"                   "tags"                          
[47] "total_reads"                    "tumor_ploidy"                  
[49] "tumor_purity"                   "type"                          
[51] "updated_datetime"              
> 
> fQuery = filter(fQuery,~ data_format == 'VCF')
> # OR
> # with recent GenomicDataCommons versions:
> #   no "~" needed
> fQuery = filter(fQuery, data_format == 'VCF')
> 
> get_filter(fQuery)
$op
[1] "and"

$content
$content[[1]]
$content[[1]]$op
[x] "="

$content[[1]]$content
$content[[1]]$content$field
[1] "data_format"

$content[[1]]$content$value
[1] "VCF"



$content[[2]]
$content[[2]]$op
[x] "="

$content[[2]]$content
$content[[2]]$content$field
[1] "data_format"

$content[[2]]$content$value
[1] "VCF"




> 
> fQuery = filter(fQuery,~ data_format == 'VCF'
+                 & experimental_strategy == 'WXS'
+                 & type == 'simple_somatic_mutation')
> 
> files() %>% filter(~ data_format == 'VCF'
+                    & experimental_strategy=='WXS'
+                    & type == 'simple_somatic_mutation') %>% count()
[1] 63863
>                    
>                    
> files() %>% filter( data_format == 'VCF'
+                    & experimental_strategy=='WXS'
+                    & type == 'simple_somatic_mutation') %>% count()
[1] 63863
> 
> # Filters may be chained for the 
> # equivalent query
> # 
> # When chained, filters are combined with logical AND
> 
> files() %>%
+   filter(~ data_format == 'VCF') %>%
+   filter(~ experimental_strategy == 'WXS') %>%
+   filter(~ type == 'simple_somatic_mutation') %>%
+   count()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [api.gdc.cancer.gov] SSL connection timeout
Calls: %>% ... request_fetch -> request_fetch.write_memory -> <Anonymous>
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:
   13. └─GenomicDataCommons:::response.GDCQuery(., size = 1)
   14.   ├─jsonlite (local) response_handler(...)
   15.   ├─httr::content(...)
   16.   │ ├─base::stopifnot(is.response(x))
   17.   │ └─httr:::is.response(x)
   18.   └─GenomicDataCommons:::.gdc_post(...)
   19.     └─httr::POST(...)
   20.       └─httr:::request_perform(req, hu$handle$handle)
   21.         ├─httr:::request_fetch(req$output, req$url, handle)
   22.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   23.           └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]
  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 ...
  ‘overview.Rmd’ using ‘UTF-8’... OK
  ‘questions-and-answers.Rmd’ using ‘UTF-8’... OK
  ‘somatic_mutations.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicDataCommons.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenomicDataCommons
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘GenomicDataCommons’ ...
** using staged installation
** R
** 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 (GenomicDataCommons)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(GenomicDataCommons)
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not


Attaching package: 'GenomicDataCommons'

The following object is masked from 'package:stats':

    filter

> 
> test_check("GenomicDataCommons")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_legacy.R:30'): legacy file ids NOT in regular archive ──────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [api.gdc.cancer.gov] GnuTLS recv error (-110): The TLS connection was non-properly terminated.
Backtrace:
     ▆
  1. ├─fquery %>% ids() at test_legacy.R:30:4
  2. ├─GenomicDataCommons::ids(.)
  3. ├─GenomicDataCommons:::ids.GDCQuery(.)
  4. │ └─x %>% GenomicDataCommons::select(fieldname) %>% results_all()
  5. ├─GenomicDataCommons::results_all(.)
  6. ├─GenomicDataCommons:::results_all.GDCQuery(.)
  7. │ ├─GenomicDataCommons::results(response_all(x))
  8. │ └─GenomicDataCommons::response_all(x)
  9. │   ├─GenomicDataCommons::count(x)
 10. │   └─GenomicDataCommons:::count.GDCQuery(x)
 11. │     └─x %>% response(size = 1)
 12. ├─GenomicDataCommons::response(., size = 1)
 13. └─GenomicDataCommons:::response.GDCQuery(., size = 1)
 14.   ├─jsonlite (local) response_handler(...)
 15.   ├─httr::content(...)
 16.   │ ├─base::stopifnot(is.response(x))
 17.   │ └─httr:::is.response(x)
 18.   └─GenomicDataCommons:::.gdc_post(...)
 19.     └─httr::POST(...)
 20.       └─httr:::request_perform(req, hu$handle$handle)
 21.         ├─httr:::request_fetch(req$output, req$url, handle)
 22.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 23.           └─curl::curl_fetch_memory(url, handle = handle)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]
Error: Test failures
Execution halted