Package: DEGseq

Version: 1.7.1

Command: mkdir DEGseq.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGseq.buildbin-libdir DEGseq_1.7.1.tar.gz >DEGseq-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=DEGseq.buildbin-libdir --install="check:DEGseq-install.out" --force-multiarch --no-vignettes --timings DEGseq_1.7.1.tar.gz && mv DEGseq.buildbin-libdir/* DEGseq.Rcheck/ && rmdir DEGseq.buildbin-libdir

StartedAt: 2011-07-07 04:46:38 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:50:24 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 226.4 seconds

RetCode: 0

Status:  OK

CheckDir: DEGseq.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/DEGseq.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 'DEGseq/DESCRIPTION' ... OK
* this is package 'DEGseq' version '1.7.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'DEGseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
    libs      1.4Mb
* 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 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 'DEGseq' ...
** libs
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c getGeneExp.cpp -o getGeneExp.o
g++ -shared -s -static-libgcc -o DEGseq.dll tmp.def getGeneExp.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/DEGseq.buildbin-libdir/DEGseq/libs/i386
** R
** inst
** preparing package for lazy loading
Loading Tcl/Tk interface ... done
Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
Loading required package: latticeExtra
Loading required package: RColorBrewer
Loading required package: impute
Loading required package: matrixStats
Loading required package: R.methodsS3
R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help.
matrixStats v0.2.2 (2010-10-06) successfully loaded. See ?matrixStats for help.
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'DEGseq.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'DEGseq' ...
** libs
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c getGeneExp.cpp -o getGeneExp.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o DEGseq.dll tmp.def getGeneExp.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/DEGseq.buildbin-libdir/DEGseq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEGseq' as DEGseq_1.7.1.zip

* DONE (DEGseq)

name	user	system	elapsed
DEGexp	2.21	0.06	2.30
DEGexp2	4.06	0.05	4.10
DEGseq	0.53	0.01	0.58
DEGseq.aln	1.26	0.46	2.26
getGeneExp	0.21	0.00	0.20
getGeneExp.aln	0.56	0.20	1.23
readGeneExp	0.03	0.00	0.03
samWrapper	4.80	0.00	4.86