Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2022-04-13 12:05:40 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for NanoStringQCPro on nebbiolo2


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? 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 1267/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringQCPro 1.26.0  (landing page)
Robert Ziman
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/NanoStringQCPro
git_branch: RELEASE_3_14
git_last_commit: 42d2b8e
git_last_commit_date: 2021-10-26 12:20:01 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.26.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NanoStringQCPro_1.26.0.tar.gz
StartedAt: 2022-04-12 08:26:02 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:28:10 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 128.1 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoStringQCPro.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NanoStringQCPro_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/NanoStringQCPro.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.26.0’
* 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 10.104  0.373  10.479
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/NanoStringQCPro.Rcheck/00check.log’
for details.



Installation output

NanoStringQCPro.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL NanoStringQCPro
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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-class0.3780.0070.386
addCodesetAnnotation0.1780.0010.179
buildCodesetAnnotation0.0080.0000.008
checkRccSet0.0330.0070.041
contentNorm0.0960.0120.107
copyRccSet0.0110.0000.011
getBackground0.0590.0080.067
getBlankLabel0.0020.0000.002
makeQCReport10.104 0.37310.479
newRccSet0.1940.0270.221
posCtrlNorm0.0160.0000.015
preprocRccSet0.0990.0000.099
presAbsCall0.0350.0040.039
readCdrDesignData0.0020.0000.002
readRcc0.0030.0000.003
readRlf0.0030.0000.003
subtractBackground0.0500.0030.055