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This page was generated on 2024-04-17 11:37:09 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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

Package 1625/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpcrNorm 1.60.0  (landing page)
Jessica Mar
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/qpcrNorm
git_branch: RELEASE_3_18
git_last_commit: 93f1931
git_last_commit_date: 2023-10-24 09:41:44 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for qpcrNorm on palomino4


To the developers/maintainers of the qpcrNorm package:
- 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 Troubleshooting Build Report for more information.
- 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: qpcrNorm
Version: 1.60.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qpcrNorm.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings qpcrNorm_1.60.0.tar.gz
StartedAt: 2024-04-16 04:00:49 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 04:01:33 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 44.3 seconds
RetCode: 0
Status:   OK  
CheckDir: qpcrNorm.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:qpcrNorm.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings qpcrNorm_1.60.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/qpcrNorm.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'qpcrNorm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qpcrNorm' version '1.60.0'
* 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 '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 sizes of PDF files under 'inst/doc' ... 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
  'F:/biocbuild/bbs-3.18-bioc/meat/qpcrNorm.Rcheck/00check.log'
for details.



Installation output

qpcrNorm.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL qpcrNorm
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-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
calcCV0.590.250.84
ctQc000
matrixByPlate0.080.030.11
normQpcrHouseKeepingGenes000
normQpcrQuantile0.080.030.11
normQpcrRankInvariant0.390.050.44
plotVarMean000
qpcrBatch-class0.000.010.01
qpcrBatch.object0.000.020.02
readQpcr000
readQpcrBatch000
writeQpcr000