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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RTCGA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RTCGA_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/RTCGA.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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") :
  URL 'http://gdac.broadinstitute.org/runs/': status was 'Couldn't connect to server'
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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/RTCGA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RTCGA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘RTCGA’ ...
** using staged installation
** R
** 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 (RTCGA)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(RTCGA)
Welcome to the RTCGA (version: 1.26.0).
> library(RTCGA.rnaseq)
> library(Biobase)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(GenomicRanges)
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> #library(RTCGA.CNV)
> #library(RTCGA.PANCAN12)
> 
> test_check("RTCGA")
[ FAIL 4 | WARN 3 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_check.R:2'): checkTCGA() function works properly ───────────────
Error in `file(con, "r")`: cannot open the connection to 'http://gdac.broadinstitute.org/runs/'
Backtrace:
    ▆
 1. ├─testthat::expect_equal(length(checkTCGA("Dates")) >= 60, T) at test_check.R:2:4
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. ├─RTCGA::checkTCGA("Dates")
 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)
── Error ('test_download.R:24'): downloadTCGA() function works properly ────────
Error in `file(con, "r")`: cannot open the connection to 'http://gdac.broadinstitute.org/runs/'
Backtrace:
    ▆
 1. ├─RTCGA (local) expect_size_equal(list("ACC", "2015-06-01"), 151456) at test_download.R:24:4
 2. │ └─RTCGA::downloadTCGA(...) at test_download.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)
── Error ('test_info.R:2'): infoTCGA() function works properly ─────────────────
<XML_IO_LOAD_ERROR/XML_IO_Error/XMLError/simpleError/error/condition>
Error: failed to load external entity "http://gdac.broadinstitute.org/"

Backtrace:
     ▆
  1. ├─testthat::expect_equal(dim(infoTCGA()), c(38, 13)) at test_info.R:2:4
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─RTCGA::infoTCGA()
  5. │ ├─base::do.call(rbind, readHTMLTable("http://gdac.broadinstitute.org/")[-39])
  6. │ ├─XML::readHTMLTable("http://gdac.broadinstitute.org/")
  7. │ └─XML::readHTMLTable("http://gdac.broadinstitute.org/")
  8. │   └─XML (local) .local(...)
  9. │     └─XML::htmlParse(doc, encoding = encoding)
 10. └─XML (local) `<fn>`(...)
── Error ('test_read.R:23'): downloadTCGA() function works properly ────────────
Error in `file(con, "r")`: cannot open the connection to 'http://gdac.broadinstitute.org/runs/'
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