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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TCGAbiolinks_2.20.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘2.20.1’
* 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  5.6Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   3.7Mb
* 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 ... WARNING
'::' or ':::' import not declared from: ‘sesameData’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GDCquery : <anonymous>: no visible binding for global variable
  ‘submitter_id’
GDCquery : <anonymous>: no visible binding for global variable
  ‘is_ffpe’
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 global function definition for
  ‘values’
readExonQuantification: no visible binding for global variable ‘exon’
readExonQuantification: no visible binding for global variable
  ‘coordinates’
readGeneExpressionQuantification : <anonymous>: no visible binding for
  '<<-' assignment to ‘assay.list’
readGeneExpressionQuantification: no visible binding for global
  variable ‘assay.list’
Undefined global functions or variables:
  Tumor.purity assay.list barcode clinical coordinates exon is_ffpe
  rse_gene submitter_id value values
* 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 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_LevelTab      15.315  0.043  15.359
GDCquery_clinic           13.345  0.683  31.403
TCGAanalyze_DEA           13.059  0.179  13.237
TCGAanalyze_Filtering     11.187  0.104  11.292
TCGAvisualize_PCA          6.675  0.064   6.740
TCGAanalyze_Stemness       6.656  0.068   6.724
TCGAanalyze_Normalization  6.321  0.168   6.489
GDCdownload                2.452  0.323  38.457
GDCprepare_clinic          1.929  0.172  47.475
matchedMetExp              0.592  0.011   5.007
GDCquery                   0.586  0.008   5.525
getResults                 0.542  0.010   5.458
getManifest                0.494  0.009   6.670
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.