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BioC 3.4: CHECK report for EasyqpcR on malbec1

This page was generated on 2017-04-15 16:11:03 -0400 (Sat, 15 Apr 2017).

Package 355/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EasyqpcR 1.16.0
Le Pape Sylvain
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/EasyqpcR
Last Changed Rev: 123122 / Revision: 128728
Last Changed Date: 2016-10-27 17:58:05 -0400 (Thu, 27 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EasyqpcR
Version: 1.16.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings EasyqpcR_1.16.0.tar.gz
StartedAt: 2017-04-14 22:14:13 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:14:49 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 36.4 seconds
RetCode: 0
Status:  OK 
CheckDir: EasyqpcR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings EasyqpcR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/EasyqpcR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EasyqpcR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EasyqpcR’ version ‘1.16.0’
* checking package namespace information ... NOTE
  Namespace with empty importFrom: ‘gWidgetsRGtk2’
* 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 ‘EasyqpcR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... 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
badCt: no visible global function definition for ‘aggregate’
nrmData: no visible global function definition for ‘aggregate’
nrmData: no visible binding for global variable ‘sd’
slope: no visible global function definition for ‘aggregate’
slope: no visible global function definition for ‘coef’
slope: no visible global function definition for ‘lm’
slope: no visible global function definition for ‘combn’
totData: no visible global function definition for ‘aggregate’
totData: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate coef combn lm sd
Consider adding
  importFrom("stats", "aggregate", "coef", "lm", "sd")
  importFrom("utils", "combn")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘vignette_EasyqpcR.toc’
Please remove them from your package.
* 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-3.4-bioc/meat/EasyqpcR.Rcheck/00check.log’
for details.


EasyqpcR.Rcheck/00install.out:

* installing *source* package ‘EasyqpcR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (EasyqpcR)

EasyqpcR.Rcheck/EasyqpcR-Ex.timings:

nameusersystemelapsed
Efficiency_calculation0.0120.0000.013
Gene_maximisation0.0000.0040.002
Gene_maximisation_cor0.0000.0000.001
badCt0.0160.0000.016
calData0.1520.0000.154
nrmData0.0800.0040.082
qPCR_run10.0000.0000.001
qPCR_run20.0040.0000.001
qPCR_run30.0000.0000.001
slope0.0080.0000.009
totData0.3800.0040.383