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BioC 3.4: CHECK report for EasyqpcR on moscato1

This page was generated on 2016-09-21 03:44:19 -0700 (Wed, 21 Sep 2016).

Package 346/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EasyqpcR 1.15.0
Le Pape Sylvain
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EasyqpcR
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: 1.15.0
Command: rm -rf EasyqpcR.buildbin-libdir EasyqpcR.Rcheck && mkdir EasyqpcR.buildbin-libdir EasyqpcR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EasyqpcR.buildbin-libdir EasyqpcR_1.15.0.tar.gz >EasyqpcR.Rcheck\00install.out 2>&1 && cp EasyqpcR.Rcheck\00install.out EasyqpcR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=EasyqpcR.buildbin-libdir --install="check:EasyqpcR-install.out" --force-multiarch --no-vignettes --timings EasyqpcR_1.15.0.tar.gz
StartedAt: 2016-09-20 07:32:40 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:34:03 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 83.1 seconds
RetCode: 0
Status:  OK  
CheckDir: EasyqpcR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf EasyqpcR.buildbin-libdir EasyqpcR.Rcheck && mkdir EasyqpcR.buildbin-libdir EasyqpcR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EasyqpcR.buildbin-libdir EasyqpcR_1.15.0.tar.gz >EasyqpcR.Rcheck\00install.out 2>&1 && cp EasyqpcR.Rcheck\00install.out EasyqpcR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=EasyqpcR.buildbin-libdir --install="check:EasyqpcR-install.out" --force-multiarch --no-vignettes --timings EasyqpcR_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/EasyqpcR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EasyqpcR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EasyqpcR' version '1.15.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'D:/biocbld/bbs-3.4-bioc/meat/EasyqpcR.Rcheck/00check.log'
for details.


EasyqpcR.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'EasyqpcR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EasyqpcR' as EasyqpcR_1.15.0.zip
* DONE (EasyqpcR)

EasyqpcR.Rcheck/examples_i386/EasyqpcR-Ex.timings:

nameusersystemelapsed
Efficiency_calculation0.080.000.08
Gene_maximisation000
Gene_maximisation_cor000
badCt0.010.020.03
calData0.180.000.17
nrmData0.090.000.10
qPCR_run1000
qPCR_run2000
qPCR_run3000
slope0.000.010.01
totData0.390.000.39

EasyqpcR.Rcheck/examples_x64/EasyqpcR-Ex.timings:

nameusersystemelapsed
Efficiency_calculation0.160.000.16
Gene_maximisation0.000.020.01
Gene_maximisation_cor000
badCt0.030.020.05
calData0.390.010.40
nrmData0.150.000.16
qPCR_run10.020.000.01
qPCR_run2000
qPCR_run3000
slope0.000.020.02
totData0.580.010.59