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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:phantasus.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings phantasus_1.15.4.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/phantasus.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 'phantasus/DESCRIPTION' ... OK
* this is package 'phantasus' version '1.15.4'
* 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 'phantasus' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 28.9Mb
  sub-directories of 1Mb or more:
    testdata   5.0Mb
    www       23.4Mb
* checking package 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 ... NOTE
Unexported objects imported by ':::' calls:
  'GEOquery:::.parseGPLTxt' 'GEOquery:::getDirListing'
  'opencpu:::rookhandler' 'opencpu:::tmp_root' 'opencpu:::win_or_mac'
  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
generatePreloadedSession: no visible binding for global variable 'es'
generatePreloadedSession: no visible binding for global variable
  'heatmapJson'
getCountsMetaPart: no visible binding for global variable 'file_name'
loadCounts: no visible global function definition for '.'
loadCounts: no visible binding for global variable 'directory'
loadCounts: no visible binding for global variable 'DT_counts_meta'
loadCounts: no visible binding for global variable 'accession'
loadCounts: no visible binding for global variable 'collection_type'
loadCounts: no visible binding for global variable 'file_name'
loadSession: no visible binding for global variable 'es'
safeDownload: no visible binding for global variable 'tempDestFile'
validateCountsCollection: no visible binding for global variable
  'file_name'
Undefined global functions or variables:
  . DT_counts_meta accession collection_type directory es file_name
  heatmapJson tempDestFile
* checking Rd files ... NOTE
prepare_Rd: convertByAnnotationDB.Rd:36-41: Dropping empty section \examples
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
getGSE 3.78   1.44   14.62
* 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:
  `expected`: TRUE 
  -- Failure (testcounts.R:115:5): updateCountsMeta create good meta files for archs4 --
  file.exists(arch_meta_file) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  -- Error (testcounts.R:116:5): updateCountsMeta create good meta files for archs4 --
  Error in `fread(arch_meta_file)`: File 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpcbMivb/test_counts/counts/archs4/meta.txt' does not exist or is non-readable. getwd()=='D:/biocbuild/bbs-3.15-bioc/meat/phantasus.Rcheck/tests/testthat'
  Backtrace:
      x
   1. \-data.table::fread(arch_meta_file) at testcounts.R:116:4
  
  [ FAIL 4 | WARN 9 | SKIP 0 | PASS 110 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/phantasus.Rcheck/00check.log'
for details.