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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:RTCGA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RTCGA_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RTCGA.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCGA/DESCRIPTION’ ... OK
* this is package ‘RTCGA’ version ‘1.35.0’
* 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 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 whether startup messages can be suppressed ... 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 ... NOTE
Unknown packages ‘RTCGA.rnaseq.20160128’, ‘RTCGA.clinical.20160128’, ‘RTCGA.mutations.20160128’, ‘RTCGA.CNV.20160128’, ‘RTCGA.RPPA.20160128’, ‘RTCGA.mRNA.20160128’, ‘RTCGA.miRNASeq.20160128’, ‘RTCGA.methylation.20160128’ in Rd xrefs
* 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')
Error in function (type, msg, asError = TRUE)  : SSL connection timeout
Calls: checkTCGA ... availableDataSets -> getURL -> curlPerform -> <Anonymous> -> fun
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:
  ── Error ('test_read.R:4:9'): downloadTCGA() function works properly ───────────
  Error in `download.file(url = paste0(filesParentURL, "/", linkToData), 
      destfile = file.path(destDir, linkToData))`: cannot open URL 'https://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601//gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
  Backtrace:
      ▆
   1. └─RTCGA (local) expect_dimsSize_equal(list("ACC", "2015-06-01"), c(92, 1115)) at test_read.R:23:5
   2.   └─RTCGA::downloadTCGA(...) at test_read.R:4:9
   3.     └─base::sapply(...)
   4.       └─base::lapply(X = X, FUN = FUN, ...)
   5.         └─RTCGA (local) FUN(X[[i]], ...)
   6.           └─utils::download.file(...)
  
  [ FAIL 3 | WARN 1 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/RTCGA.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL RTCGA
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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: 1.35.0). Read more about the project under https://rtcga.github.io/RTCGA/
> 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, aperm, 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, 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 object is masked from 'package:utils':

    findMatches

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")
trying URL 'https://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601//gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Content type 'application/x-gzip' length 151456 bytes (147 KB)
==================================================
downloaded 147 KB

trying URL 'https://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601//gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 4 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_check.R:2:5'): checkTCGA() function works properly ─────────────
Error in `open.connection(x, "rb")`: Timeout was reached: [gdac.broadinstitute.org] SSL connection timeout
Backtrace:
     ▆
  1. ├─testthat::expect_equal(length(checkTCGA("Dates")) >= 60, T) at test_check.R:2:5
  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. │   ├─... %>% ...
  7. │   ├─xml2::read_html("https://gdac.broadinstitute.org/runs/stddata__latest/")
  8. │   └─xml2:::read_html.default("https://gdac.broadinstitute.org/runs/stddata__latest/")
  9. │     ├─base::suppressWarnings(...)
 10. │     │ └─base::withCallingHandlers(...)
 11. │     ├─xml2::read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
 12. │     └─xml2:::read_xml.character(...)
 13. │       └─xml2:::read_xml.connection(...)
 14. │         ├─base::open(x, "rb")
 15. │         └─base::open.connection(x, "rb")
 16. ├─base::assign(x = ".lastWorkingDate", value = ., envir = .RTCGAEnv)
 17. ├─base::gsub(., pattern = "_", replacement = "-", fixed = TRUE)
 18. │ └─base::is.factor(x)
 19. ├─base::substring(., first = 1, last = 10)
 20. ├─rvest::html_text(.)
 21. │ └─xml2::xml_text(x, trim = trim)
 22. └─rvest::html_nodes(., "h3")
 23.   └─rvest::html_elements(...)
── Error ('test_info.R:4:5'): infoTCGA() function works properly ───────────────
<OPERATION_TIMEDOUT/GenericCurlError/error/condition>
Error in `function (type, msg, asError = TRUE) 
{
    if (!is.character(type)) {
        i = match(type, CURLcodeValues)
        typeName = if (is.na(i)) 
            character()
        else names(CURLcodeValues)[i]
    }
    typeName = gsub("^CURLE_", "", typeName)
    fun = (if (asError) 
        stop
    else warning)
    fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
        "GenericCurlError", "error", "condition")))
}(28L, "SSL connection timeout", TRUE)`: SSL connection timeout
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test_info.R:4:5
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─"ACC" %in% (sub("-counts", "", x = rownames(infoTCGA())))
  5. ├─base::sub("-counts", "", x = rownames(infoTCGA()))
  6. │ └─base::is.factor(x)
  7. ├─base::rownames(infoTCGA())
  8. │ └─dimnames(x)[[1L]] %||% ...
  9. ├─RTCGA::infoTCGA()
 10. │ └─RCurl::getURL("https://gdac.broadinstitute.org/", .opts = list(ssl.verifypeer = FALSE))
 11. │   └─RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
 12. └─RCurl (local) `<fn>`(28L, "SSL connection timeout", TRUE)
── Error ('test_read.R:4:9'): downloadTCGA() function works properly ───────────
Error in `download.file(url = paste0(filesParentURL, "/", linkToData), 
    destfile = file.path(destDir, linkToData))`: cannot open URL 'https://gdac.broadinstitute.org/runs/stddata__2015_06_01/data/ACC/20150601//gdac.broadinstitute.org_ACC.Merge_Clinical.Level_1.2015060100.0.0.tar.gz'
Backtrace:
    ▆
 1. └─RTCGA (local) expect_dimsSize_equal(list("ACC", "2015-06-01"), c(92, 1115)) at test_read.R:23:5
 2.   └─RTCGA::downloadTCGA(...) at test_read.R:4:9
 3.     └─base::sapply(...)
 4.       └─base::lapply(X = X, FUN = FUN, ...)
 5.         └─RTCGA (local) FUN(X[[i]], ...)
 6.           └─utils::download.file(...)

[ FAIL 3 | WARN 1 | SKIP 0 | PASS 4 ]
Error: Test failures
Execution halted