* using log directory 'd:/Rcompile/CRANpkg/local/3.5/aroma.affymetrix.Rcheck'
* using R Under development (unstable) (2018-02-21 r74285)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'aroma.affymetrix/DESCRIPTION' ... OK
* this is package 'aroma.affymetrix' version '3.1.0'
* 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 'aroma.affymetrix' can be installed ... WARNING
Found the following significant warnings:
  Note: break may be used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/aroma.affymetrix.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
* 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [123s] OK
* 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 examples ... [3s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [35s] ERROR
  Running '001.setupExampleData,annotationData.R' [18s]
  Running '002.setupExampleData,rawData.R' [4s]
  Running 'AffymetrixCdfFile.R' [5s]
  Running 'AffymetrixCelFile.R' [3s]
  Running 'AffymetrixCelSet.R' [4s]
Running the tests in 'tests/002.setupExampleData,rawData.R' failed.
Last 13 lines of output:
    at #03. createLink(link = pathnameD, target = pathnameS, skip = TRUE)
            - createLink() is in environment 'R.utils'
  
    at #02. setupExampleData.AromaAffymetrix(aroma.affymetrix, dirs = "rawData", 
                mustWork = FALSE)
            - setupExampleData.AromaAffymetrix() is in environment 'aroma.affymetrix'
  
    at #01. setupExampleData(aroma.affymetrix, dirs = "rawData", mustWork = FALSE)
            - setupExampleData() is in environment 'aroma.affymetrix'
  
  Error: Failed to create file link: rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-1-121502.CEL[.lnk] -> D:/temp/Rtmp2Pm9wL/RLIBS_1876c64aa2e2e/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL
  In addition: Warning message:
  In system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  :
    running command 'C:\Windows\system32\cmd.exe /c mklink "rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-1-121502.CEL" "D:/temp/Rtmp2Pm9wL/RLIBS_1876c64aa2e2e/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL"' had status 1
  Execution halted
Running the tests in 'tests/AffymetrixCdfFile.R' failed.
Last 13 lines of output:
            - createLink() is in environment 'R.utils'
  
    at #02. setupExampleData.AromaAffymetrix(aroma.affymetrix, dataset = "FusionSDK_Test3", 
                dirs = "annotationData", mustWork = FALSE)
            - setupExampleData.AromaAffymetrix() is in environment 'aroma.affymetrix'
  
    at #01. setupExampleData(aroma.affymetrix, dataset = "FusionSDK_Test3", 
                dirs = "annotationData", mustWork = FALSE)
            - setupExampleData() is in environment 'aroma.affymetrix'
  
  Error: Failed to create file link: annotationData/chipTypes/Test3/Test3.CDF[.lnk] -> D:/temp/Rtmp2Pm9wL/RLIBS_1876c64aa2e2e/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF
  In addition: Warning message:
  In system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  :
    running command 'C:\Windows\system32\cmd.exe /c mklink "annotationData/chipTypes/Test3/Test3.CDF" "D:/temp/Rtmp2Pm9wL/RLIBS_1876c64aa2e2e/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF"' had status 1
  Execution halted
Running the tests in 'tests/AffymetrixCelSet.R' failed.
Last 13 lines of output:
  
    at #04. createLink.default(link = pathnameD, target = pathnameS, skip = TRUE)
            - createLink.default() is in environment 'R.utils'
  
    at #03. createLink(link = pathnameD, target = pathnameS, skip = TRUE)
            - createLink() is in environment 'R.utils'
  
    at #02. setupExampleData.AromaAffymetrix(aroma.affymetrix, mustWork = FALSE)
            - setupExampleData.AromaAffymetrix() is in environment 'aroma.affymetrix'
  
    at #01. setupExampleData(aroma.affymetrix, mustWork = FALSE)
            - setupExampleData() is in environment 'aroma.affymetrix'
  
  Error: Pathname not found: rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-1-121502.CEL (rawData/FusionSDK_HG-Focus/HG-Focus/ exists, but nothing beyond; current directory is 'd:/Rcompile/CRANpkg/local/3.5/aroma.affymetrix.Rcheck/tests')
  Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE