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BioC 3.0: CHECK report for GeneMeta on moscato1

This page was generated on 2015-04-10 09:43:51 -0700 (Fri, 10 Apr 2015).

Package 349/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneMeta 1.38.0
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GeneMeta
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: GeneMeta
Version: 1.38.0
Command: rm -rf GeneMeta.buildbin-libdir GeneMeta.Rcheck && mkdir GeneMeta.buildbin-libdir GeneMeta.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneMeta.buildbin-libdir GeneMeta_1.38.0.tar.gz >GeneMeta.Rcheck\00install.out 2>&1 && cp GeneMeta.Rcheck\00install.out GeneMeta-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GeneMeta.buildbin-libdir --install="check:GeneMeta-install.out" --force-multiarch --no-vignettes --timings GeneMeta_1.38.0.tar.gz
StartedAt: 2015-04-10 01:24:39 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:27:14 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 154.7 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneMeta.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GeneMeta.buildbin-libdir GeneMeta.Rcheck && mkdir GeneMeta.buildbin-libdir GeneMeta.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneMeta.buildbin-libdir GeneMeta_1.38.0.tar.gz >GeneMeta.Rcheck\00install.out 2>&1 && cp GeneMeta.Rcheck\00install.out GeneMeta-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GeneMeta.buildbin-libdir --install="check:GeneMeta-install.out" --force-multiarch --no-vignettes --timings GeneMeta_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/GeneMeta.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneMeta/DESCRIPTION' ... OK
* this is package 'GeneMeta' version '1.38.0'
* 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 'GeneMeta' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' '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
* 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 ... NOTE
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'genefilter'
  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
File 'GeneMeta/R/meta1.R':
  .onLoad calls:
    require("methods")

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

getdF_matrix: no visible global function definition for 'rowttests'
* checking Rd files ... NOTE
prepare_Rd: CountPlot.Rd:39: Dropping empty section \keyword
prepare_Rd: CountPlot.Rd:30: Dropping empty section \value
prepare_Rd: CountPlot.Rd:38: Dropping empty section \examples
prepare_Rd: tau.Rd:25: Dropping empty section \details
prepare_Rd: tau.Rd:26: Dropping empty section \value
* 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' ... [6s] OK
** running examples for arch 'x64' ... [7s] 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/GeneMeta.Rcheck/00check.log'
for details.

GeneMeta.Rcheck/00install.out:


install for i386

* installing *source* package 'GeneMeta' ...
** 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 'GeneMeta' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneMeta' as GeneMeta_1.38.0.zip
* DONE (GeneMeta)

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

nameusersystemelapsed
Nevins0.390.030.42
dstar0.010.000.01
f.Q000
tau000
zscore0.690.000.69

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

nameusersystemelapsed
Nevins0.420.000.42
dstar000
f.Q000
tau000
zscore0.800.000.81