Package: VanillaICE

Version: 1.13.3

Command: /Users/biocbuild/BBS/utils/build-universal.sh VanillaICE_1.13.3.tar.gz /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R VanillaICE.buildbin-libdir

StartedAt: 2011-02-24 17:29:13 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 17:29:21 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 8.7 seconds

RetCode: 0

Status:  OK

PackageFile: VanillaICE_1.13.3.tgz

PackageFileSize: 2.035 MiB

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=VanillaICE.buildbin-libdir VanillaICE_1.13.3.tar.gz'
>>>>>>> 

* installing *source* package 'VanillaICE' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c viterbi.c -o viterbi.o
viterbi.c: In function 'viterbi':
viterbi.c:61: warning: unused variable 'tp'
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o VanillaICE.so viterbi.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/VanillaICE.buildbin-libdir/VanillaICE/libs/i386
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c viterbi.c -o viterbi.o
viterbi.c: In function 'viterbi':
viterbi.c:61: warning: unused variable 'tp'
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o VanillaICE.so viterbi.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/VanillaICE.buildbin-libdir/VanillaICE/libs/ppc
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c viterbi.c -o viterbi.o
viterbi.c: In function 'viterbi':
viterbi.c:61: warning: unused variable 'tp'
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o VanillaICE.so viterbi.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/VanillaICE.buildbin-libdir/VanillaICE/libs/x86_64
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: oligoClasses
================================================================================
Welcome to oligoClasses version 1.13.9
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Loading package bit1.1-6

package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)

creators: bit bitwhich

coercion: as.logical as.integer as.bit as.bitwhich which

operator: ! & | xor != == 

querying: print length any all min max range sum summary

bit access: length<- [ [<- [[ [[<-

for more help type ?bit

Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Loading package ff2.2-1

- getOption("fftempdir")=="/tmp/RtmpuVc6Vu"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system

Welcome to crlmm version 1.9.14

Attaching package: 'IRanges'

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

    updateObject

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

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Welcome to VanillaICE version 1.13.3

* DONE (VanillaICE)


>>>>>>> 
>>>>>>> FIXING LINKS FOR VanillaICE.buildbin-libdir/VanillaICE/libs/i386/VanillaICE.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/i386/VanillaICE.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/i386/VanillaICE.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/i386/VanillaICE.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/i386/VanillaICE.so"


>>>>>>> 
>>>>>>> FIXING LINKS FOR VanillaICE.buildbin-libdir/VanillaICE/libs/ppc/VanillaICE.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/ppc/VanillaICE.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/ppc/VanillaICE.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/ppc/VanillaICE.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/ppc/VanillaICE.so"


>>>>>>> 
>>>>>>> FIXING LINKS FOR VanillaICE.buildbin-libdir/VanillaICE/libs/x86_64/VanillaICE.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/x86_64/VanillaICE.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/x86_64/VanillaICE.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/x86_64/VanillaICE.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "VanillaICE.buildbin-libdir/VanillaICE/libs/x86_64/VanillaICE.so"