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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1356/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringQCPro 1.32.0  (landing page)
Robert Ziman
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/NanoStringQCPro
git_branch: RELEASE_3_17
git_last_commit: 2529d9b
git_last_commit_date: 2023-04-25 10:39:06 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    ERROR    OK  

CHECK results for NanoStringQCPro on kjohnson2


To the developers/maintainers of the NanoStringQCPro package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: NanoStringQCPro
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoStringQCPro_1.32.0.tar.gz
StartedAt: 2023-10-18 10:56:13 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 11:00:40 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 266.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: NanoStringQCPro.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoStringQCPro_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/NanoStringQCPro.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* 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 for sufficient/correct file permissions ... 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 ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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 = "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/NanoStringQCPro/misc/qcReportHeader.html")
Calls: makeQCReport ... makeQCReport -> .local -> knit2html -> mark_html -> <Anonymous>
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/NanoStringQCPro.Rcheck/00check.log’
for details.


Installation output

NanoStringQCPro.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NanoStringQCPro
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)

Tests output


Example timings

NanoStringQCPro.Rcheck/NanoStringQCPro-Ex.timings

nameusersystemelapsed
RccSet-class0.4580.0150.719
addCodesetAnnotation0.2760.0190.435
buildCodesetAnnotation0.0090.0020.013
checkRccSet0.0470.0010.079
contentNorm0.1190.0030.173
copyRccSet0.0150.0020.020
getBackground0.0730.0030.094
getBlankLabel0.0010.0020.004