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Package 136/553HostnameOS / ArchBUILDCHECKBUILD BIN
cummeRbund 1.2.0
Loyal A. Goff
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/cummeRbund
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: cummeRbund
Version: 1.2.0
Command: rm -rf cummeRbund.buildbin-libdir && mkdir cummeRbund.buildbin-libdir && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cummeRbund.buildbin-libdir cummeRbund_1.2.0.tar.gz >cummeRbund-install.out 2>&1 && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD check --library=cummeRbund.buildbin-libdir --install="check:cummeRbund-install.out" --force-multiarch --no-vignettes --timings cummeRbund_1.2.0.tar.gz && mv cummeRbund.buildbin-libdir/* cummeRbund.Rcheck/ && rmdir cummeRbund.buildbin-libdir
StartedAt: 2012-09-24 00:20:32 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:21:42 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 70.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cummeRbund.Rcheck
Warnings: 2

Command output

* using log directory 'E:/biocbld/bbs-2.10-bioc/meat/cummeRbund.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cummeRbund/DESCRIPTION' ... OK
* this is package 'cummeRbund' version '1.2.0'
* 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 whether package 'cummeRbund' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
.MAplot: no visible binding for global variable 'A'
.MAplot: no visible binding for global variable 'M'
.barplot: no visible binding for global variable 'sample_name'
.barplot: no visible binding for global variable 'conf_lo'
.barplot: no visible binding for global variable 'conf_hi'
.barplot: no visible binding for global variable 'quant_status'
.boxplot: no visible binding for global variable 'sample_name'
.density: no visible binding for global variable 'sample_name'
.expressionPlot: no visible binding for global variable 'sample_name'
.expressionPlot: no visible binding for global variable 'tracking_id'
.expressionPlot: no visible binding for global variable 'conf_lo'
.expressionPlot: no visible binding for global variable 'conf_hi'
.expressionPlot: no visible binding for global variable 'quant_status'
.ggheat: no visible binding for global variable 'colInd'
.ggheat: no visible binding for global variable 'rowInd'
.ggheat: no visible binding for global variable 'value'
.heatmap: no visible binding for global variable 'tracking_id'
.heatmap: no visible binding for global variable 'sample_name'
.volcano: no visible binding for global variable 'log2_fold_change'
.volcano: no visible binding for global variable 'p_value'
.volcano: no visible binding for global variable 'significant'
csClusterPlot: no visible binding for global variable 'variable'
csClusterPlot: no visible binding for global variable 'value'
csClusterPlot: no visible binding for global variable 'cluster'
csClusterPlot: no visible binding for global variable 'ids'
* 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 examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:

  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_blank' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_line' is deprecated.
  Warning: 'theme_line' is deprecated.
  Warning: 'theme_rect' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_blank' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_line' is deprecated.
  Warning: 'theme_line' is deprecated.
  Warning: 'theme_rect' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.10-bioc/meat/cummeRbund.Rcheck/00check.log'
for details.

cummeRbund.Rcheck/00install.out:


install for i386

* installing *source* package 'cummeRbund' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'cummeRbund-manual.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'cummeRbund' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cummeRbund' as cummeRbund_1.2.0.zip

* DONE (cummeRbund)