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BioC 3.3: CHECK report for BrainStars on moscato2

This page was generated on 2016-10-13 12:50:32 -0700 (Thu, 13 Oct 2016).

Package 128/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BrainStars 1.16.0
Itoshi NIKAIDO
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/BrainStars
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BrainStars
Version: 1.16.0
Command: rm -rf BrainStars.buildbin-libdir BrainStars.Rcheck && mkdir BrainStars.buildbin-libdir BrainStars.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BrainStars.buildbin-libdir BrainStars_1.16.0.tar.gz >BrainStars.Rcheck\00install.out 2>&1 && cp BrainStars.Rcheck\00install.out BrainStars-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=BrainStars.buildbin-libdir --install="check:BrainStars-install.out" --force-multiarch --no-vignettes --timings BrainStars_1.16.0.tar.gz
StartedAt: 2016-10-13 01:34:45 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:36:11 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 86.0 seconds
RetCode: 0
Status:  OK  
CheckDir: BrainStars.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BrainStars.buildbin-libdir BrainStars.Rcheck && mkdir BrainStars.buildbin-libdir BrainStars.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BrainStars.buildbin-libdir BrainStars_1.16.0.tar.gz >BrainStars.Rcheck\00install.out 2>&1 && cp BrainStars.Rcheck\00install.out BrainStars-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=BrainStars.buildbin-libdir --install="check:BrainStars-install.out" --force-multiarch --no-vignettes --timings BrainStars_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/BrainStars.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 'BrainStars/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BrainStars' version '1.16.0'
* 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 'BrainStars' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
A package should be listed in only one of these fields.
* 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 ... NOTE
Packages in Depends field not imported from:
  'RCurl' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getBrainStarsExpression: no visible global function definition for
  'read.csv'
getBrainStars: no visible global function definition for 'getURL'
getBrainStarsExpression: no visible global function definition for
  'new'
getBrainStarsFigure: no visible global function definition for
  'getBinaryURL'
Undefined global functions or variables:
  getBinaryURL getURL new read.csv
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
getBrainStarsFigure 0.14   0.01    8.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
getBrainStarsFigure 0.12      0    8.89
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/BrainStars.Rcheck/00check.log'
for details.


BrainStars.Rcheck/00install.out:


install for i386

* installing *source* package 'BrainStars' ...
** 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 'BrainStars' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BrainStars' as BrainStars_1.16.0.zip
* DONE (BrainStars)

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

nameusersystemelapsed
getBrainStars0.470.104.41
getBrainStarsFigure0.140.018.91

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

nameusersystemelapsed
getBrainStars0.510.004.41
getBrainStarsFigure0.120.008.89