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BioC 3.4: CHECK report for SigFuge on tokay1

This page was generated on 2017-04-15 16:18:01 -0400 (Sat, 15 Apr 2017).

Package 1141/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SigFuge 1.12.0
Patrick Kimes
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/SigFuge
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: SigFuge
Version: 1.12.0
Command: rm -rf SigFuge.buildbin-libdir SigFuge.Rcheck && mkdir SigFuge.buildbin-libdir SigFuge.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SigFuge.buildbin-libdir SigFuge_1.12.0.tar.gz >SigFuge.Rcheck\00install.out 2>&1 && cp SigFuge.Rcheck\00install.out SigFuge-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SigFuge.buildbin-libdir --install="check:SigFuge-install.out" --force-multiarch --no-vignettes --timings SigFuge_1.12.0.tar.gz
StartedAt: 2017-04-15 00:49:47 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:53:04 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 197.9 seconds
RetCode: 0
Status:  OK  
CheckDir: SigFuge.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SigFuge.buildbin-libdir SigFuge.Rcheck && mkdir SigFuge.buildbin-libdir SigFuge.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SigFuge.buildbin-libdir SigFuge_1.12.0.tar.gz >SigFuge.Rcheck\00install.out 2>&1 && cp SigFuge.Rcheck\00install.out SigFuge-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SigFuge.buildbin-libdir --install="check:SigFuge-install.out" --force-multiarch --no-vignettes --timings SigFuge_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/SigFuge.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 'SigFuge/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SigFuge' version '1.12.0'
* 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 'SigFuge' 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
SFfigure: no visible binding for global variable 'base'
SFfigure: no visible binding for global variable 's'
SFfigure: no visible binding for global variable 'e'
SFfigure: no visible global function definition for 'rgb'
SFfigure: no visible global function definition for 'hcl'
SFfigure: no visible binding for global variable 'cluster'
SFfigure: no visible binding for global variable 'median'
SFfigure: no visible binding for global variable 'x'
SFfigure: no visible binding for global variable 'y1'
SFfigure: no visible binding for global variable 'label'
SFfigure: no visible binding for global variable 'value'
SFfigure: no visible binding for global variable 'Clusters'
SFfigure: no visible binding for global variable 'y2'
SFfigure: no visible global function definition for 'pdf'
SFfigure: no visible global function definition for 'dev.off'
SFlabels: no visible global function definition for 'kmeans'
SFnormalize : <anonymous>: no visible global function definition for
  'median'
Undefined global functions or variables:
  Clusters base cluster dev.off e hcl kmeans label median pdf rgb s
  value x y1 y2
Consider adding
  importFrom("grDevices", "dev.off", "hcl", "pdf", "rgb")
  importFrom("stats", "kmeans", "median")
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 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
SFfigure 23.52   0.42   23.94
SFpval   13.68   0.82   14.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
SFfigure 21.11   0.34   21.47
SFpval   13.41   0.77   14.17
* 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/SigFuge.Rcheck/00check.log'
for details.


SigFuge.Rcheck/00install.out:


install for i386

* installing *source* package 'SigFuge' ...
** 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 'SigFuge' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SigFuge' as SigFuge_1.12.0.zip
* DONE (SigFuge)

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

nameusersystemelapsed
SFfigure23.52 0.4223.94
SFlabels1.420.081.50
SFnormalize0.140.020.16
SFpval13.68 0.8214.52

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

nameusersystemelapsed
SFfigure21.11 0.3421.47
SFlabels1.780.111.89
SFnormalize0.250.000.25
SFpval13.41 0.7714.17