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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoStringQCPro.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings NanoStringQCPro_1.32.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/NanoStringQCPro.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 'NanoStringQCPro/DESCRIPTION' ... OK
* this is package 'NanoStringQCPro' version '1.32.0'
* 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 'NanoStringQCPro' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'NanoStringQCPro' is deprecated and will be removed from
See 'F:/biocbuild/bbs-3.17-bioc/meat/NanoStringQCPro.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'knitr'
A package should be listed in only one of these fields.
* 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
centeredSampleClustering: no visible global function definition for
  'png'
centeredSampleClustering: no visible global function definition for
  'dev.off'
countsInBlankSamples_verticalPlot: no visible global function
  definition for 'png'
countsInBlankSamples_verticalPlot: no visible global function
  definition for 'dev.off'
geneClustering: no visible global function definition for 'png'
geneClustering: no visible global function definition for 'dev.off'
negCtrlsByLane_verticalPlot: no visible global function definition for
  'png'
negCtrlsByLane_verticalPlot: no visible global function definition for
  'dev.off'
previewPNG: no visible global function definition for 'png'
previewPNG: no visible global function definition for 'dev.off'
sampleClustering,RccSet: no visible global function definition for
  'png'
sampleClustering,RccSet: no visible global function definition for
  'dev.off'
Undefined global functions or variables:
  dev.off png
Consider adding
  importFrom("grDevices", "dev.off", "png")
to your NAMESPACE file.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... ERROR
Running examples in 'NanoStringQCPro-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeQCReport,RccSet-method
> ### Title: Make NanoString QC report
> ### Aliases: makeQCReport,RccSet-method makeQCReport
> 
> ### ** Examples
> 
> data(example_rccSet)
> norm_example_rccSet <- preprocRccSet(example_rccSet)
> qc_example_rccSet <- makeQCReport(norm_example_rccSet, "example_QC_report")
Generating QC report...
Error in mark(..., format = "html", template = template) : 
  unused argument (header = "F:/biocbuild/bbs-3.17-bioc/R/library/NanoStringQCPro/misc/qcReportHeader.html")
Calls: makeQCReport -> makeQCReport -> .local -> knit2html -> <Anonymous>
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/NanoStringQCPro.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL NanoStringQCPro
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'NanoStringQCPro' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: Package 'NanoStringQCPro' is deprecated and will be removed from
  Bioconductor version 3.18
** testing if installed package can be loaded from final location
Warning: Package 'NanoStringQCPro' is deprecated and will be removed from
  Bioconductor version 3.18
** testing if installed package keeps a record of temporary installation path
* DONE (NanoStringQCPro)