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BioC 3.4: CHECK report for Roleswitch on moscato1

This page was generated on 2016-09-21 03:45:13 -0700 (Wed, 21 Sep 2016).

Package 1042/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Roleswitch 1.11.0
Yue Li
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Roleswitch
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  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Roleswitch
Version: 1.11.0
Command: rm -rf Roleswitch.buildbin-libdir Roleswitch.Rcheck && mkdir Roleswitch.buildbin-libdir Roleswitch.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Roleswitch.buildbin-libdir Roleswitch_1.11.0.tar.gz >Roleswitch.Rcheck\00install.out 2>&1 && cp Roleswitch.Rcheck\00install.out Roleswitch-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Roleswitch.buildbin-libdir --install="check:Roleswitch-install.out" --force-multiarch --no-vignettes --timings Roleswitch_1.11.0.tar.gz
StartedAt: 2016-09-20 15:43:46 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:47:52 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 245.9 seconds
RetCode: 0
Status:  OK  
CheckDir: Roleswitch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Roleswitch.buildbin-libdir Roleswitch.Rcheck && mkdir Roleswitch.buildbin-libdir Roleswitch.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Roleswitch.buildbin-libdir Roleswitch_1.11.0.tar.gz >Roleswitch.Rcheck\00install.out 2>&1 && cp Roleswitch.Rcheck\00install.out Roleswitch-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Roleswitch.buildbin-libdir --install="check:Roleswitch-install.out" --force-multiarch --no-vignettes --timings Roleswitch_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/Roleswitch.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 'Roleswitch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Roleswitch' version '1.11.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'pracma' 'reshape' 'plotrix' 'microRNA' 'biomaRt' 'Biostrings'
  'Biobase' 'DBI'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'Roleswitch' 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
* 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 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
diagnosticPlot: no visible global function definition for 'par'
diagnosticPlot: no visible global function definition for 'axis'
diagnosticPlot: no visible global function definition for 'plot'
getSeedMatrix: no visible global function definition for 'data'
getTranscriptIDwithLongest3UTR: no visible global function definition
  for 'aggregate'
roleswitch: no visible global function definition for 'aggregate'
Undefined global functions or variables:
  aggregate axis data par plot
Consider adding
  importFrom("graphics", "axis", "par", "plot")
  importFrom("stats", "aggregate")
  importFrom("utils", "data")
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
getSeedMatrix 3.06   0.24   79.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getSeedMatrix 3.33   0.17   34.01
* 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/Roleswitch.Rcheck/00check.log'
for details.


Roleswitch.Rcheck/00install.out:


install for i386

* installing *source* package 'Roleswitch' ...
** 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 'Roleswitch' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Roleswitch' as Roleswitch_1.11.0.zip
* DONE (Roleswitch)

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

nameusersystemelapsed
Roleswitch-package000
diagnosticPlot0.030.000.03
getSeedMatrix 3.06 0.2479.89
roleswitch000
tcga_gbm_testdata0.240.060.29

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

nameusersystemelapsed
Roleswitch-package000
diagnosticPlot0.030.000.03
getSeedMatrix 3.33 0.1734.01
roleswitch000
tcga_gbm_testdata0.140.090.23