BioC 2.9: CHECK report for CNTools on moscato1

Package: CNTools

Version: 1.10.0

Command: rm -rf CNTools.buildbin-libdir && mkdir CNTools.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNTools.buildbin-libdir CNTools_1.10.0.tar.gz >CNTools-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=CNTools.buildbin-libdir --install="check:CNTools-install.out" --force-multiarch --no-vignettes --timings CNTools_1.10.0.tar.gz && mv CNTools.buildbin-libdir/* CNTools.Rcheck/ && rmdir CNTools.buildbin-libdir

StartedAt: 2012-03-24 01:00:18 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:02:17 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 119.6 seconds

RetCode: 0

Status: OK

CheckDir: CNTools.Rcheck

Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/CNTools.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNTools/DESCRIPTION' ... OK
* this is package 'CNTools' version '1.10.0'
* 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 'CNTools' 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
File 'CNTools/R/zzz.R':
  .onLoad calls:
    require("methods", quietly = TRUE)
    require("tools", quietly = TRUE)

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

* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                 old_size new_size compress
  geneInfo.rda      503Kb    335Kb       xz
  sampleData.rda    521Kb    411Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK


install for i386

* installing *source* package 'CNTools' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c getratios.c -o getratios.o
gcc -shared -s -static-libgcc -o CNTools.dll tmp.def getratios.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/CNTools.buildbin-libdir/CNTools/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'start' in package 'CNTools'
Creating a new generic function for 'end' in package 'CNTools'
Creating a generic function for 'genefilter' from package 'genefilter' in package 'CNTools'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'HowTo.Rnw' 
** testing if installed package can be loaded
Warning in library.dynam("CNTools", package = "CNTools") :
  use of library.dynam() without specifying both 'package' and 'lib.loc' is deprecated

add DLL for x64

* installing *source* package 'CNTools' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c getratios.c -o getratios.o
gcc -m64 -shared -s -static-libgcc -o CNTools.dll tmp.def getratios.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/CNTools.buildbin-libdir/CNTools/libs/x64
** testing if installed package can be loaded
Warning in library.dynam("CNTools", package = "CNTools") :
  use of library.dynam() without specifying both 'package' and 'lib.loc' is deprecated
* MD5 sums
packaged installation of 'CNTools' as CNTools_1.10.0.zip

* DONE (CNTools)

Summary

Command output