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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAbiolinks.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.28.4.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/TCGAbiolinks.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TCGAbiolinks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCGAbiolinks' version '2.28.4'
* 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 whether package 'TCGAbiolinks' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   4.5Mb
* 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 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
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 ... 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_DEA      11.30   0.33   11.62
getManifest           8.84   0.14   88.56
TCGAanalyze_LevelTab  6.06   0.14    6.21
GDCprepare_clinic     0.92   0.20   28.59
matchedMetExp         0.92   0.01    8.41
GDCquery              0.66   0.09    6.37
getResults            0.61   0.03    5.79
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/TCGAbiolinks.Rcheck/00check.log'
for details.