Package: ChIPseqR

Version: 1.7.0

Command: mkdir ChIPseqR.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPseqR.buildbin-libdir ChIPseqR_1.7.0.tar.gz >ChIPseqR-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=ChIPseqR.buildbin-libdir --install="check:ChIPseqR-install.out" --force-multiarch --no-vignettes --timings ChIPseqR_1.7.0.tar.gz && mv ChIPseqR.buildbin-libdir/* ChIPseqR.Rcheck/ && rmdir ChIPseqR.buildbin-libdir

StartedAt: 2011-07-07 04:33:47 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:41:08 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 440.8 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPseqR.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/ChIPseqR.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 'ChIPseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPseqR' version '1.7.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ChIPseqR' 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 ... NOTE
prepare_Rd: startScore.Rd:38: Dropping empty section \references
* 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 'ChIPseqR' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:15: warning: unused variable 'tmp_stat'
gcc -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/i386
** R
** inst
** preparing package for lazy loading
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
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Introduction.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'ChIPseqR' ...
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c startScore.c -o startScore.o
startScore.c: In function '_ratioStat_pois':
startScore.c:66:15: warning: unused variable 'tmp_stat'
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o ChIPseqR.dll tmp.def startScore.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/ChIPseqR.buildbin-libdir/ChIPseqR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPseqR' as ChIPseqR_1.7.0.zip

* DONE (ChIPseqR)

name	user	system	elapsed
BindScore	18.40	0.28	18.68
ChIPseqR-package	0.00	0.00	0.01
RLEBindScore-class	16.43	0.41	16.84
RLEReadCounts-class	0.03	0.00	0.03
ReadCounts	0.03	0.00	0.03
alignFeature	26.79	1.32	28.11
callBindingSites	16.14	0.28	16.44
pos2gff	0	0	0
simpleNucCall	14.06	0.19	14.25
strandPileup	0.01	0.00	0.01
windowCounts	0.05	0.00	0.05