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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RTCGA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RTCGA_1.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RTCGA.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 ‘RTCGA/DESCRIPTION’ ... OK
* this is package ‘RTCGA’ version ‘1.29.0’
* 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 ... 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: boxplotTCGA
> ### Title: Create Boxplots for TCGA Datasets
> ### Aliases: boxplotTCGA
> 
> ### ** Examples
> 
> library(RTCGA)
> library(RTCGA.rnaseq)
> # perfrom plot
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> expressionsTCGA(ACC.rnaseq, BLCA.rnaseq, BRCA.rnaseq, OV.rnaseq,
+   extract.cols = "MET|4233") %>%
+   rename(cohort = dataset,
+   MET = `MET|4233`) %>%  
+   #cancer samples
+   filter(substr(bcr_patient_barcode, 14, 15) == "01") -> ACC_BLCA_BRCA_OV.rnaseq
>   
> 
> boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "cohort", "MET")
> boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "cohort", "log1p(MET)")
> boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)")
> boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), max)", "log1p(MET)")
> boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)",
+             xlab = "Cohort Type", ylab = "Logarithm of MET")
> boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)", 
+             xlab = "Cohort Type", ylab = "Logarithm of MET", legend.title = "Cohorts")
> boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)", 
+             xlab = "Cohort Type", ylab = "Logarithm of MET", 
+             legend.title = "Cohorts", legend = "bottom")
> 
> ## facet example
> library(RTCGA.mutations)
> library(dplyr)
> mutationsTCGA(BRCA.mutations, OV.mutations, ACC.mutations, BLCA.mutations) %>% 
+   filter(Hugo_Symbol == 'TP53') %>%
+   filter(substr(bcr_patient_barcode, 14, 15) == "01") %>% # cancer tissue
+   mutate(bcr_patient_barcode = substr(bcr_patient_barcode, 1, 12)) -> 
+   ACC_BLCA_BRCA_OV.mutations
Killed
* 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:
  
      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
  
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘RTCGA_Workflow.Rmd’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RTCGA
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 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(RTCGA)
Welcome to the RTCGA (version: 1.29.0). 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, 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")
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

Killed