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This page was generated on 2021-10-15 15:05:46 -0400 (Fri, 15 Oct 2021).

CHECK results for NanoStringQCPro on nebbiolo1

To the developers/maintainers of the NanoStringQCPro package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoStringQCPro.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1247/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringQCPro 1.24.0  (landing page)
Robert Ziman
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/NanoStringQCPro
git_branch: RELEASE_3_13
git_last_commit: 1366855
git_last_commit_date: 2021-05-19 12:12:54 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NanoStringQCPro
Version: 1.24.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings NanoStringQCPro_1.24.0.tar.gz
StartedAt: 2021-10-14 10:46:35 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:48:40 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 124.9 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoStringQCPro.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings NanoStringQCPro_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/NanoStringQCPro.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoStringQCPro/DESCRIPTION’ ... OK
* this is package ‘NanoStringQCPro’ version ‘1.24.0’
* 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 ... OK
* 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 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
makeQCReport 10.049  0.364  10.415
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/NanoStringQCPro.Rcheck/00check.log’
for details.



Installation output

NanoStringQCPro.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL NanoStringQCPro
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (NanoStringQCPro)

Tests output


Example timings

NanoStringQCPro.Rcheck/NanoStringQCPro-Ex.timings

nameusersystemelapsed
RccSet-class0.3460.0110.358
addCodesetAnnotation0.1920.0040.202
buildCodesetAnnotation0.0080.0000.009
checkRccSet0.0350.0040.039
contentNorm0.0870.0040.091
copyRccSet0.0240.0000.024
getBackground0.0620.0000.062
getBlankLabel0.0020.0000.001
makeQCReport10.049 0.36410.415
newRccSet0.1930.0120.205
posCtrlNorm0.0120.0040.016
preprocRccSet0.1170.0080.126
presAbsCall0.0350.0000.035
readCdrDesignData0.0010.0000.002
readRcc0.0030.0000.003
readRlf0.0030.0000.002
subtractBackground0.0490.0000.049