BioC 2.9: CHECK report for mosaics on moscato1

Package: mosaics

Version: 1.2.5

Command: rm -rf mosaics.buildbin-libdir && mkdir mosaics.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mosaics.buildbin-libdir mosaics_1.2.5.tar.gz >mosaics-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=mosaics.buildbin-libdir --install="check:mosaics-install.out" --force-multiarch --no-vignettes --timings mosaics_1.2.5.tar.gz && mv mosaics.buildbin-libdir/* mosaics.Rcheck/ && rmdir mosaics.buildbin-libdir

StartedAt: 2012-03-24 02:10:26 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:12:36 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 129.6 seconds

RetCode: 0

Status: OK

CheckDir: mosaics.Rcheck

Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/mosaics.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 'mosaics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mosaics' version '1.2.5'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'mosaics' 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
mosaicsRunAll: no visible global function definition for 'mclapply'
readBins: no visible global function definition for 'mclapply'
* 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 compilation flags in Makevars ... 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 'mosaics' ...
** libs
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include"      -O2 -Wall  -mtune=core2 -c convolution_1S.cpp -o convolution_1S.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include"      -O2 -Wall  -mtune=core2 -c convolution_2S.cpp -o convolution_2S.o
g++ -shared -s -static-libgcc -o mosaics.dll tmp.def convolution_1S.o convolution_2S.o D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/lib/i386/libRcpp.a -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/mosaics.buildbin-libdir/mosaics/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'print' from package 'base' in package 'mosaics'
Creating a generic function for 'plot' from package 'graphics' in package 'mosaics'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'mosaics-example.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'mosaics' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c convolution_1S.cpp -o convolution_1S.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c convolution_2S.cpp -o convolution_2S.o
g++ -m64 -shared -s -static-libgcc -o mosaics.dll tmp.def convolution_1S.o convolution_2S.o D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/lib/x64/libRcpp.a -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/mosaics.buildbin-libdir/mosaics/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mosaics' as mosaics_1.2.5.zip

* DONE (mosaics)

Summary

Command output