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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TCGAbiolinks_2.31.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/TCGAbiolinks.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.31.4’
* 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 ‘TCGAbiolinks’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   4.3Mb
* 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 ... WARNING
'::' or ':::' import not declared from: ‘dnet’
* checking S3 generic/method consistency ... WARNING
print:
  function(x, ...)
print.header:
  function(text, type)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GDCprepare_clinic: no visible binding for global variable
  ‘bcr_patient_barcode’
GDCprepare_clinic: no visible binding for global variable
  ‘days_to_last_followup’
GDCprepare_clinic: no visible binding for global variable
  ‘vital_status’
GDCquery : <anonymous>: no visible binding for global variable
  ‘submitter_id’
GDCquery : <anonymous>: no visible binding for global variable
  ‘is_ffpe’
GDCquery_clinic : <anonymous>: no visible binding for global variable
  ‘submitter_id’
GDCquery_clinic : <anonymous>: no visible global function definition
  for ‘across’
GDCquery_clinic : <anonymous>: no visible global function definition
  for ‘everything’
TCGAanalyze_DEA: no visible binding for global variable ‘barcode’
TCGAanalyze_DEA: no visible binding for global variable ‘clinical’
TCGAquery_recount2: no visible binding for global variable ‘rse_gene’
TCGAtumor_purity: no visible binding for global variable ‘Tumor.purity’
TCGAvisualize_oncoprint: no visible binding for global variable ‘value’
TCGAvisualize_starburst: no visible binding for global variable
  ‘gene_name’
TCGAvisualize_starburst: no visible binding for global variable
  ‘geFDR2’
TCGAvisualize_starburst: no visible binding for global variable ‘logFC’
TCGAvisualize_starburst: no visible binding for global variable
  ‘meFDR2’
TCGAvisualize_starburst: no visible binding for global variable
  ‘threshold.starburst’
TCGAvisualize_starburst: no visible binding for global variable
  ‘starburst.status’
colDataPrepare: no visible binding for global variable
  ‘sample_submitter_id’
colDataPrepare: no visible binding for global variable ‘submitter_id’
readExonQuantification: no visible binding for global variable ‘exon’
readExonQuantification: no visible binding for global variable
  ‘coordinates’
readSingleCellAnalysis : <anonymous>: no visible global function
  definition for ‘Read10X’
read_gene_expression_quantification : <anonymous>: no visible binding
  for '<<-' assignment to ‘assay.list’
read_gene_expression_quantification: no visible binding for global
  variable ‘assay.list’
Undefined global functions or variables:
  Read10X Tumor.purity across assay.list barcode bcr_patient_barcode
  clinical coordinates days_to_last_followup everything exon geFDR2
  gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id
  starburst.status submitter_id threshold.starburst value vital_status
* checking Rd files ... NOTE
checkRd: (-1) geneInfoHT.Rd:12: Lost braces; missing escapes or markup?
    12 | ```{R, eval = F}
       |    ^
checkRd: (-1) geneInfoHT.Rd:21-33: Lost braces
    21 | geneInfoHT <- plyr::adply(seq(1,length(biomart_getID$ensembl_gene_id),step),.margins = 1,.fun = function(x){
       |                                                                                                            ^
checkRd: (-1) geneInfoHT.Rd:26-29: Lost braces
    26 |     if(!file.exists(file)){
       |                           ^
checkRd: (-1) geneInfoHT.Rd:29-31: Lost braces
    29 |     } else {
       |            ^
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
TCGAanalyze_DEA   10.339  0.788  11.128
getManifest        9.836  1.090  90.200
GDCprepare_clinic  2.183  0.258  30.180
matchedMetExp      1.629  0.186  12.440
GDCquery           1.208  0.160   8.576
getResults         0.901  0.056   6.417
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL TCGAbiolinks
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘TCGAbiolinks’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (TCGAbiolinks)

R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(TCGAbiolinks)
> 
> test_check("TCGAbiolinks")

|                                                    |  0%                      
|==========================                          | 50% ~0 s remaining       
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|==========================                          | 50% ~0 s remaining       
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 
[1] "I need about  1 minute to finish complete  Enrichment analysis GO[BP,MF,CC] and Pathways... "
[1] "GO Enrichment Analysis BP completed....done"
[1] "GO Enrichment Analysis MF completed....done"
[1] "GO Enrichment Analysis CC completed....done"
[1] "Pathway Enrichment Analysis completed....done"
[ FAIL 0 | WARN 0 | SKIP 24 | PASS 32 ]

══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On Bioconductor (24): 'test-prepare-download.R:4:5',
  'test-prepare-download.R:49:5', 'test-prepare-download.R:92:5',
  'test-prepare-download.R:102:5', 'test-prepare-download.R:124:5',
  'test-prepare-download.R:145:5', 'test-prepare-download.R:164:5',
  'test-prepare-download.R:183:5', 'test-prepare-download.R:199:5',
  'test-prepare-download.R:209:5', 'test-prepare-download.R:221:5',
  'test-prepare-download.R:246:5', 'test-prepare-download.R:286:5',
  'test-prepare-download.R:316:5', 'test-prepare-download.R:347:5',
  'test-prepare-download.R:381:5', 'test-query-clinical.R:13:5',
  'test-query-clinical.R:69:5', 'test-query.R:5:5', 'test-query.R:15:5',
  'test-query.R:44:5', 'test-query.R:86:5', 'test-query.R:127:5',
  'test-query.R:147:5'

[ FAIL 0 | WARN 0 | SKIP 24 | PASS 32 ]
> 
> proc.time()
   user  system elapsed 
 44.488   1.548  46.028