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BioC experimental data: CHECK report for yeastCC on moscato2

This page was generated on 2013-10-08 16:07:22 -0700 (Tue, 08 Oct 2013).

Package 152/156HostnameOS / ArchBUILDCHECKBUILD BIN
yeastCC 1.2.18
Sandrine Dudoit
Snapshot Date: 2013-10-08 10:15:19 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/yeastCC
Last Changed Rev: 2317 / Revision: 2510
Last Changed Date: 2013-04-03 15:11:40 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: yeastCC
Version: 1.2.18
Command: rm -rf yeastCC.buildbin-libdir && mkdir yeastCC.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=yeastCC.buildbin-libdir yeastCC_1.2.18.tar.gz >yeastCC-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=yeastCC.buildbin-libdir --install="check:yeastCC-install.out" --force-multiarch --no-vignettes --timings yeastCC_1.2.18.tar.gz && mv yeastCC.buildbin-libdir/* yeastCC.Rcheck/ && rmdir yeastCC.buildbin-libdir
StartedAt: 2013-10-08 14:01:10 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 14:04:11 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 180.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: yeastCC.Rcheck
Warnings: 6

Command output

* using log directory 'E:/biocbld/bbs-2.12-data-experiment/meat/yeastCC.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'yeastCC/DESCRIPTION' ... OK
* this is package 'yeastCC' version '1.2.18'
* 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 'yeastCC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    2.6Mb
* checking package 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 ... WARNING
Found directory 'R' with no source files.
* 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 ... WARNING
Error in tools:::.check_packages_used(package = "yeastCC") : 
  directory 'E:/biocbld/bbs-2.12-data-experiment/meat/yeastCC.buildbin-libdir/yeastCC' does not contain R code
Execution halted
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
Error in tools::checkS3methods(package = "yeastCC") : 
  directory 'E:/biocbld/bbs-2.12-data-experiment/meat/yeastCC.buildbin-libdir/yeastCC' does not contain R code
Execution halted
See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
Error in tools::checkReplaceFuns(package = "yeastCC") : 
  directory 'E:/biocbld/bbs-2.12-data-experiment/meat/yeastCC.buildbin-libdir/yeastCC' does not contain R code
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... NOTE
Error in tools::checkFF(package = "yeastCC") : 
  directory 'E:/biocbld/bbs-2.12-data-experiment/meat/yeastCC.buildbin-libdir/yeastCC' does not contain R code
Execution halted
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Error in tools::codoc(package = "yeastCC") : 
  directory 'E:/biocbld/bbs-2.12-data-experiment/meat/yeastCC.buildbin-libdir/yeastCC' does not contain R code
Execution halted
Error in tools::codocClasses(package = "yeastCC") : 
  directory 'E:/biocbld/bbs-2.12-data-experiment/meat/yeastCC.buildbin-libdir/yeastCC' does not contain R code
Execution halted
* checking Rd \usage sections ... NOTE
Error in tools::checkDocStyle(package = "yeastCC") : 
  directory 'E:/biocbld/bbs-2.12-data-experiment/meat/yeastCC.buildbin-libdir/yeastCC' does not contain R code
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... WARNING
  Warning: large data file saved inefficiently:
                 size ASCII compress
  spYCCmeta.rda 430Kb FALSE     none
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                old_size new_size compress
  breeden.rda      1.9Mb    1.5Mb       xz
  spYCCES.rda      757Kb    484Kb       xz
  spYCCmeta.rda    430Kb     55Kb       xz
  yeastCC.rda      1.5Mb    484Kb       xz
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [2s] OK
* checking PDF version of manual ... OK

WARNING: There were 6 warnings.
NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.12-data-experiment/meat/yeastCC.Rcheck/00check.log'
for details.

yeastCC.Rcheck/00install.out:


install for i386

* installing *source* package 'yeastCC' ...
** data
*** moving datasets to lazyload DB
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'yeastCC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'yeastCC' as yeastCC_1.2.18.zip
* DONE (yeastCC)