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This page was generated on 2022-04-13 12:05:48 -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 qpcrNorm on nebbiolo2


To the developers/maintainers of the qpcrNorm package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qpcrNorm.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 1498/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpcrNorm 1.52.0  (landing page)
Jessica Mar
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/qpcrNorm
git_branch: RELEASE_3_14
git_last_commit: 3c4c33e
git_last_commit_date: 2021-10-26 11:53:47 -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: qpcrNorm
Version: 1.52.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:qpcrNorm.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings qpcrNorm_1.52.0.tar.gz
StartedAt: 2022-04-12 08:53:14 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:53:43 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 28.3 seconds
RetCode: 0
Status:   OK  
CheckDir: qpcrNorm.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:qpcrNorm.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings qpcrNorm_1.52.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/qpcrNorm.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 ‘qpcrNorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qpcrNorm’ version ‘1.52.0’
* 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 ‘qpcrNorm’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘affy’ ‘limma’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘Biobase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcCV : <anonymous>: no visible global function definition for ‘sd’
normQpcrRankInvariant: no visible global function definition for
  ‘median’
normQpcrRankInvariant: no visible binding for global variable ‘median’
plotVarMean: no visible binding for global variable ‘var’
plotVarMean: no visible global function definition for ‘abline’
plotVarMean: no visible global function definition for ‘lines’
plotVarMean: no visible global function definition for ‘lowess’
readQpcr: no visible global function definition for ‘read.table’
writeQpcr: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline lines lowess median read.table sd var write.table
Consider adding
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "lowess", "median", "sd", "var")
  importFrom("utils", "read.table", "write.table")
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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/qpcrNorm.Rcheck/00check.log’
for details.



Installation output

qpcrNorm.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘qpcrNorm’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (qpcrNorm)

Tests output


Example timings

qpcrNorm.Rcheck/qpcrNorm-Ex.timings

nameusersystemelapsed
calcCV0.5280.0280.556
ctQc000
matrixByPlate0.0760.0000.075
normQpcrHouseKeepingGenes0.0050.0000.005
normQpcrQuantile0.0810.0040.085
normQpcrRankInvariant0.3370.0000.338
plotVarMean000
qpcrBatch-class0.0040.0000.004
qpcrBatch.object0.0010.0030.004
readQpcr000
readQpcrBatch000
writeQpcr000