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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TCGAbiolinks.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TCGAbiolinks_2.23.5.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/TCGAbiolinks.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TCGAbiolinks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCGAbiolinks' version '2.23.5'
* 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  5.9Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   3.4Mb
* 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 ':::' imports not declared from:
  'Seurat' 'SeuratDisk' 'sesameData'
':::' call which should be '::': 'stringr:::str_split'
  See the note in ?`:::` about the use of this operator.
* 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'
readSingleCellAnalysis : <anonymous>: no visible global function
  definition for 'Read10X'
Undefined global functions or variables:
  Read10X 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
GDCquery_clinic        15.43   0.19   35.36
TCGAanalyze_DEA        13.08   0.25   13.33
TCGAanalyze_Filtering  10.19   0.10   10.30
TCGAanalyze_LevelTab    7.91   0.16    8.06
TCGAvisualize_PCA       5.18   0.03    5.21
GDCdownload             2.55   0.23   33.00
GDCprepare_clinic       1.75   0.13   41.36
getDataCategorySummary  1.15   0.02    5.90
GDCquery                0.46   0.00    5.32
getResults              0.38   0.01    5.97
matchedMetExp           0.39   0.00    5.58
getManifest             0.37   0.00    6.44
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/TCGAbiolinks.Rcheck/00check.log'
for details.