BioC 2.9: CHECK report for Ringo on moscato1

Package: Ringo

Version: 1.18.0

Command: rm -rf Ringo.buildbin-libdir && mkdir Ringo.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Ringo.buildbin-libdir Ringo_1.18.0.tar.gz >Ringo-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=Ringo.buildbin-libdir --install="check:Ringo-install.out" --force-multiarch --no-vignettes --timings Ringo_1.18.0.tar.gz && mv Ringo.buildbin-libdir/* Ringo.Rcheck/ && rmdir Ringo.buildbin-libdir

StartedAt: 2012-03-24 02:44:04 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:47:46 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 222.2 seconds

RetCode: 0

Status: OK

CheckDir: Ringo.Rcheck

Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/Ringo.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 'Ringo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Ringo' version '1.18.0'
* 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 'Ringo' 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 'Ringo/R/zzz.R':
  .onAttach calls:
    require(Biobase)

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

exportCherList: no visible global function definition for 'IRanges'
oneChannelVSN: no visible global function definition for 'vsnMatrix'
sigGOTable: no visible binding for global variable 'p.value'
* 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 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 'Ringo' ...
** libs
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c mmeansd.cpp -o mmeansd.o
mmeansd.cpp: In function 'SEXPREC* moving_mean_sd(SEXP, SEXP, SEXP)':
mmeansd.cpp:27:24: warning: variable 'is' set but not used [-Wunused-but-set-variable]
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c mmedian.cpp -o mmedian.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c region_overlap.c -o region_overlap.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c ringo_init.c -o ringo_init.o
g++ -shared -s -static-libgcc -o Ringo.dll tmp.def mmeansd.o mmedian.o region_overlap.o ringo_init.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/Ringo.buildbin-libdir/Ringo/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'Ringo'
Creating a generic function for 'get' from package 'base' in package 'Ringo'
Creating a generic function for 'ls' from package 'base' in package 'Ringo'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Ringo.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'Ringo' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mmeansd.cpp -o mmeansd.o
mmeansd.cpp: In function 'SEXPREC* moving_mean_sd(SEXP, SEXP, SEXP)':
mmeansd.cpp:27:24: warning: variable 'is' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c mmedian.cpp -o mmedian.o
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 region_overlap.c -o region_overlap.o
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 ringo_init.c -o ringo_init.o
g++ -m64 -shared -s -static-libgcc -o Ringo.dll tmp.def mmeansd.o mmedian.o region_overlap.o ringo_init.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/Ringo.buildbin-libdir/Ringo/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Ringo' as Ringo_1.18.0.zip

* DONE (Ringo)

Summary

Command output