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BioC 3.4: CHECK report for ffpe on tokay1

This page was generated on 2017-04-15 16:17:09 -0400 (Sat, 15 Apr 2017).

Package 413/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ffpe 1.18.0
Levi Waldron
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/ffpe
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 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: ffpe
Version: 1.18.0
Command: rm -rf ffpe.buildbin-libdir ffpe.Rcheck && mkdir ffpe.buildbin-libdir ffpe.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ffpe.buildbin-libdir ffpe_1.18.0.tar.gz >ffpe.Rcheck\00install.out 2>&1 && cp ffpe.Rcheck\00install.out ffpe-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ffpe.buildbin-libdir --install="check:ffpe-install.out" --force-multiarch --no-vignettes --timings ffpe_1.18.0.tar.gz
StartedAt: 2017-04-14 22:17:15 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:23:03 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 348.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ffpe.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ffpe.buildbin-libdir ffpe.Rcheck && mkdir ffpe.buildbin-libdir ffpe.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ffpe.buildbin-libdir ffpe_1.18.0.tar.gz >ffpe.Rcheck\00install.out 2>&1 && cp ffpe.Rcheck\00install.out ffpe-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ffpe.buildbin-libdir --install="check:ffpe-install.out" --force-multiarch --no-vignettes --timings ffpe_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/ffpe.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ffpe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ffpe' version '1.18.0'
* 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 'ffpe' 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
CATplot: no visible global function definition for 'abline'
sampleQC,matrix : makeplots: no visible global function definition for
  'cor'
sampleQC,matrix : makeplots: no visible global function definition for
  'median'
sampleQC,matrix : makeplots: no visible binding for global variable
  'median'
sampleQC,matrix : makeplots: no visible global function definition for
  'na.omit'
sampleQC,matrix : makeplots: no visible global function definition for
  'loess'
sampleQC,matrix : makeplots: no visible global function definition for
  'predict'
sampleQC,matrix : makeplots: no visible global function definition for
  'IQR'
sampleQC,matrix : makeplots: no visible global function definition for
  'abline'
sampleQC,matrix : makeplots: no visible global function definition for
  'legend'
sampleQC,matrix : makeplots: no visible global function definition for
  'lines'
sampleQC,matrix: no visible binding for global variable 'IQR'
sampleQC,matrix: no visible global function definition for 'na.omit'
sortedIqrPlot,matrix: no visible binding for global variable 'quantile'
sortedIqrPlot,matrix: no visible global function definition for
  'segments'
sortedIqrPlot,matrix: no visible binding for global variable 'IQR'
Undefined global functions or variables:
  IQR abline cor legend lines loess median na.omit predict quantile
  segments
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "segments")
  importFrom("stats", "IQR", "cor", "loess", "median", "na.omit",
             "predict", "quantile")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
CATplot 6.71   0.18    7.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
CATplot 5.75   0.17    5.92
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/ffpe.Rcheck/00check.log'
for details.


ffpe.Rcheck/00install.out:


install for i386

* installing *source* package 'ffpe' ...
** R
** 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 'ffpe' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ffpe' as ffpe_1.18.0.zip
* DONE (ffpe)

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

nameusersystemelapsed
CATplot6.710.187.75
ffpe-package2.920.113.03
sampleQC3.630.103.72
sortedIqrPlot1.220.031.25

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

nameusersystemelapsed
CATplot5.750.175.92
ffpe-package2.840.113.06
sampleQC2.960.032.99
sortedIqrPlot0.920.040.95