BioC 2.9: CHECK report for externalVector on moscato1

Package: externalVector

Version: 1.19.0

Command: mkdir externalVector.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=externalVector.buildbin-libdir externalVector_1.19.0.tar.gz >externalVector-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=externalVector.buildbin-libdir --install="check:externalVector-install.out" --force-multiarch --no-vignettes --timings externalVector_1.19.0.tar.gz && mv externalVector.buildbin-libdir/* externalVector.Rcheck/ && rmdir externalVector.buildbin-libdir

StartedAt: 2011-07-07 04:52:06 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:53:33 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 87.3 seconds

RetCode: 0

Status: OK

CheckDir: externalVector.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/externalVector.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'externalVector/DESCRIPTION' ... OK
* this is package 'externalVector' version '1.19.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'externalVector' 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 ... 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 ... 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK


install for i386

* installing *source* package 'externalVector' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c allocator.c -o allocator.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c arraySummary.c -o arraySummary.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c coerce.c -o coerce.o
coerce.c: In function 'ComplexFromString':
coerce.c:213:18: warning: initialization from incompatible pointer type
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c externalVector.c -o externalVector.o
externalVector.c:6:1: warning: 'ScalarVector' defined but not used
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c groups.c -o groups.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c math.c -o math.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c slice.c -o slice.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c storage.c -o storage.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c subscript.c -o subscript.o
gcc -shared -s -static-libgcc -o externalVector.dll tmp.def allocator.o arraySummary.o coerce.o externalVector.o groups.o math.o slice.o storage.o subscript.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/externalVector.buildbin-libdir/externalVector/libs/i386
** R
** preparing package for lazy loading
Creating a generic function for "match" from package "base" in package "externalVector"
Creating a generic function for "as.vector" from package "base" in package "externalVector"
Creating a generic function for "as.single" from package "base" in package "externalVector"
Creating a generic function for "as.list" from package "base" in package "externalVector"
Creating a generic function for "as.matrix" from package "base" in package "externalVector"
Creating a generic function for "as.data.frame" from package "base" in package "externalVector"
Creating a generic function for "colSums" from package "base" in package "externalVector"
Creating a generic function for "colMeans" from package "base" in package "externalVector"
Creating a generic function for "rowSums" from package "base" in package "externalVector"
Creating a generic function for "rowMeans" from package "base" in package "externalVector"
Creating a generic function for "apply" from package "base" in package "externalVector"
Creating a generic function for "lapply" from package "base" in package "externalVector"
Creating a generic function for "sapply" from package "base" in package "externalVector"
Creating a generic function for "mean" from package "base" in package "externalVector"
Creating a generic function for "median" from package "stats" in package "externalVector"
Creating a new generic function for "var" in package "externalVector"
Creating a new generic function for "cov" in package "externalVector"
Creating a new generic function for "cor" in package "externalVector"
Creating a generic function for "cov2cor" from package "stats" in package "externalVector"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'externalVector' ...
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c allocator.c -o allocator.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c arraySummary.c -o arraySummary.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c coerce.c -o coerce.o
coerce.c: In function 'ComplexFromString':
coerce.c:213:18: warning: initialization from incompatible pointer type
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c externalVector.c -o externalVector.o
externalVector.c:6:1: warning: 'ScalarVector' defined but not used
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c groups.c -o groups.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c math.c -o math.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c slice.c -o slice.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c storage.c -o storage.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c subscript.c -o subscript.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o externalVector.dll tmp.def allocator.o arraySummary.o coerce.o externalVector.o groups.o math.o slice.o storage.o subscript.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/externalVector.buildbin-libdir/externalVector/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'externalVector' as externalVector_1.19.0.zip

* DONE (externalVector)

name	user	system	elapsed
SubscriptList	0	0	0
allNA	0	0	0
as.Rvector	0	0	0
asEach	0.05	0.00	0.05
defaultElement	0	0	0
externalMatrix	0.01	0.00	0.02
externalVector	0.02	0.00	0.01
gcAllocator-class	0.03	0.00	0.03
makeSlice	0	0	0
setExternalStorageClass	0	0	0
setVirtualMethod	0.06	0.00	0.06
var	0.02	0.00	0.02

Summary

Command output