Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOP[Q]RSTUVWXYZ

CHECK report for qpcrNorm on malbec1

This page was generated on 2019-04-16 11:48:43 -0400 (Tue, 16 Apr 2019).

Package 1223/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpcrNorm 1.40.0
Jessica Mar
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/qpcrNorm
Branch: RELEASE_3_8
Last Commit: 54cc773
Last Changed Date: 2018-10-30 11:41:45 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: qpcrNorm
Version: 1.40.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:qpcrNorm.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings qpcrNorm_1.40.0.tar.gz
StartedAt: 2019-04-16 02:17:52 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:18:23 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 31.0 seconds
RetCode: 0
Status:  OK 
CheckDir: qpcrNorm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:qpcrNorm.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings qpcrNorm_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/qpcrNorm.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.40.0’
* 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 ‘plot’
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 plot read.table sd var write.table
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  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-3.8-bioc/meat/qpcrNorm.Rcheck/00check.log’
for details.



Installation output

qpcrNorm.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL qpcrNorm
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘qpcrNorm’ ...
** 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
* DONE (qpcrNorm)

Tests output


Example timings

qpcrNorm.Rcheck/qpcrNorm-Ex.timings

nameusersystemelapsed
calcCV1.2960.1081.410
ctQc000
matrixByPlate0.1840.0000.185
normQpcrHouseKeepingGenes0.0080.0000.009
normQpcrQuantile0.1720.0040.178
normQpcrRankInvariant0.5160.0120.532
plotVarMean000
qpcrBatch-class0.0080.0000.005
qpcrBatch.object0.0040.0000.006
readQpcr000
readQpcrBatch000
writeQpcr000