Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M [N] O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.12: BUILD BIN report for ncdfFlow on petty

This page was generated on 2013-10-09 09:40:06 -0700 (Wed, 09 Oct 2013).

Package 436/671HostnameOS / ArchBUILDCHECKBUILD BIN
ncdfFlow 1.6.1
M. Jiang
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/ncdfFlow
Last Changed Rev: 78304 / Revision: 81334
Last Changed Date: 2013-07-10 16:03:19 -0700 (Wed, 10 Jul 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ]

Summary

Package: ncdfFlow
Version: 1.6.1
Command: rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ncdfFlow_1.6.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ncdfFlow.buildbin-libdir
StartedAt: 2013-10-09 01:00:08 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:00:33 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 24.1 seconds
RetCode: 0
Status:  OK 
PackageFile: ncdfFlow_1.6.1.tgz
PackageFileSize: 2.679 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ncdfFlow.buildbin-libdir ncdfFlow_1.6.1.tar.gz'
>>>>>>> 

* installing *source* package 'ncdfFlow' ...
removing .o files
configure: search for hdf5 library in: /usr/lib
configure: found hdf5 library in: /usr/lib
configure: using bundled netcdf4 library
configure: 'found ' trimmed_netcdf-4.2.1.1 ' header sources and tar archive;using what is there.'
configure: Using the following compilation and linking flags for ncdfFlow
configure: 	PKG_CPPFLAGS=-I/usr/include
configure: 	PKG_LIBS=-L/usr/lib -lhdf5 -lhdf5_hl
configure: creating ./config.status
config.status: creating src/Makevars
** libs
/Library/Frameworks/R.framework/Resources/share/make/shlib.mk:6: warning: overriding commands for target `ncdfFlow.so'
Makevars:32: warning: ignoring old commands for target `ncdfFlow.so'
/Library/Frameworks/R.framework/Resources/share/make/shlib.mk:6: warning: overriding commands for target `ncdfFlow.so'
Makevars:32: warning: ignoring old commands for target `ncdfFlow.so'
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c bitOps.c -o bitOps.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c netCDF.c -o netCDF.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/liblib/stub.c -o trimmed_netcdf-4.2.1.1/liblib/stub.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/datt.c -o trimmed_netcdf-4.2.1.1/libdispatch/datt.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dattget.c -o trimmed_netcdf-4.2.1.1/libdispatch/dattget.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dattinq.c -o trimmed_netcdf-4.2.1.1/libdispatch/dattinq.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dattput.c -o trimmed_netcdf-4.2.1.1/libdispatch/dattput.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dcompound.c -o trimmed_netcdf-4.2.1.1/libdispatch/dcompound.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dcopy.c -o trimmed_netcdf-4.2.1.1/libdispatch/dcopy.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/ddim.c -o trimmed_netcdf-4.2.1.1/libdispatch/ddim.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/ddispatch.c -o trimmed_netcdf-4.2.1.1/libdispatch/ddispatch.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/denum.c -o trimmed_netcdf-4.2.1.1/libdispatch/denum.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/derror.c -o trimmed_netcdf-4.2.1.1/libdispatch/derror.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dfile.c -o trimmed_netcdf-4.2.1.1/libdispatch/dfile.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dgroup.c -o trimmed_netcdf-4.2.1.1/libdispatch/dgroup.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dnclog.c -o trimmed_netcdf-4.2.1.1/libdispatch/dnclog.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dopaque.c -o trimmed_netcdf-4.2.1.1/libdispatch/dopaque.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dparallel.c -o trimmed_netcdf-4.2.1.1/libdispatch/dparallel.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dstring.c -o trimmed_netcdf-4.2.1.1/libdispatch/dstring.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dsubstrate.c -o trimmed_netcdf-4.2.1.1/libdispatch/dsubstrate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dtype.c -o trimmed_netcdf-4.2.1.1/libdispatch/dtype.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dutf8proc.c -o trimmed_netcdf-4.2.1.1/libdispatch/dutf8proc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dv2i.c -o trimmed_netcdf-4.2.1.1/libdispatch/dv2i.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dvar.c -o trimmed_netcdf-4.2.1.1/libdispatch/dvar.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dvarget.c -o trimmed_netcdf-4.2.1.1/libdispatch/dvarget.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dvarinq.c -o trimmed_netcdf-4.2.1.1/libdispatch/dvarinq.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dvarput.c -o trimmed_netcdf-4.2.1.1/libdispatch/dvarput.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/dvlen.c -o trimmed_netcdf-4.2.1.1/libdispatch/dvlen.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/nc_uri.c -o trimmed_netcdf-4.2.1.1/libdispatch/nc_uri.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/ncaux.c -o trimmed_netcdf-4.2.1.1/libdispatch/ncaux.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/ncbytes.c -o trimmed_netcdf-4.2.1.1/libdispatch/ncbytes.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/nchashmap.c -o trimmed_netcdf-4.2.1.1/libdispatch/nchashmap.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/nclist.c -o trimmed_netcdf-4.2.1.1/libdispatch/nclist.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libdispatch/nctime.c -o trimmed_netcdf-4.2.1.1/libdispatch/nctime.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/attr.c -o trimmed_netcdf-4.2.1.1/libsrc/attr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/dim.c -o trimmed_netcdf-4.2.1.1/libsrc/dim.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/lookup3.c -o trimmed_netcdf-4.2.1.1/libsrc/lookup3.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/memio.c -o trimmed_netcdf-4.2.1.1/libsrc/memio.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/nc.c -o trimmed_netcdf-4.2.1.1/libsrc/nc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/nc3dispatch.c -o trimmed_netcdf-4.2.1.1/libsrc/nc3dispatch.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/ncio.c -o trimmed_netcdf-4.2.1.1/libsrc/ncio.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/nclistmgr.c -o trimmed_netcdf-4.2.1.1/libsrc/nclistmgr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/ncx.c -o trimmed_netcdf-4.2.1.1/libsrc/ncx.o
trimmed_netcdf-4.2.1.1/libsrc/ncx.c:44:1: warning: "LONG_LONG_MAX" redefined
In file included from /usr/llvm-gcc-4.2/bin/../lib/gcc/i686-apple-darwin10/4.2.1/include/limits.h:15,
                 from trimmed_netcdf-4.2.1.1/libsrc/ncx.c:33:
/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin10/4.2.1/include/limits.h:114:1: warning: this is the location of the previous definition
trimmed_netcdf-4.2.1.1/libsrc/ncx.c:45:1: warning: "LONG_LONG_MIN" redefined
/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin10/4.2.1/include/limits.h:112:1: warning: this is the location of the previous definition
trimmed_netcdf-4.2.1.1/libsrc/ncx.c:46:1: warning: "ULONG_LONG_MAX" redefined
/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin10/4.2.1/include/limits.h:118:1: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/posixio.c -o trimmed_netcdf-4.2.1.1/libsrc/posixio.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/putget.c -o trimmed_netcdf-4.2.1.1/libsrc/putget.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/v1hpg.c -o trimmed_netcdf-4.2.1.1/libsrc/v1hpg.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc/var.c -o trimmed_netcdf-4.2.1.1/libsrc/var.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc4/error4.c -o trimmed_netcdf-4.2.1.1/libsrc4/error4.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc4/nc4attr.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4attr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc4/nc4dim.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4dim.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc4/nc4dispatch.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4dispatch.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc4/nc4file.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4file.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc4/nc4grp.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4grp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc4/nc4hdf.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4hdf.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc4/nc4internal.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4internal.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc4/nc4type.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4type.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc4/nc4var.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4var.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c trimmed_netcdf-4.2.1.1/libsrc4/ncfunc.c -o trimmed_netcdf-4.2.1.1/libsrc4/ncfunc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o ncdfFlow.so bitOps.o init.o netCDF.o trimmed_netcdf-4.2.1.1/liblib/stub.o trimmed_netcdf-4.2.1.1/libdispatch/datt.o trimmed_netcdf-4.2.1.1/libdispatch/dattget.o trimmed_netcdf-4.2.1.1/libdispatch/dattinq.o trimmed_netcdf-4.2.1.1/libdispatch/dattput.o trimmed_netcdf-4.2.1.1/libdispatch/dcompound.o trimmed_netcdf-4.2.1.1/libdispatch/dcopy.o trimmed_netcdf-4.2.1.1/libdispatch/ddim.o trimmed_netcdf-4.2.1.1/libdispatch/ddispatch.o trimmed_netcdf-4.2.1.1/libdispatch/denum.o trimmed_netcdf-4.2.1.1/libdispatch/derror.o trimmed_netcdf-4.2.1.1/libdispatch/dfile.o trimmed_netcdf-4.2.1.1/libdispatch/dgroup.o trimmed_netcdf-4.2.1.1/libdispatch/dnclog.o trimmed_netcdf-4.2.1.1/libdispatch/dopaque.o trimmed_netcdf-4.2.1.1/libdispatch/dparallel.o trimmed_netcdf-4.2.1.1/libdispatch/dstring.o trimmed_netcdf-4.2.1.1/libdispatch/dsubstrate.o trimmed_netcdf-4.2.1.1/libdispatch/dtype.o trimmed_netcdf-4.2.1.1/libdispatch/dutf8proc.o trimmed_netcdf-4.2.1.1/libdispatch/dv2i.o trimmed_netcdf-4.2.1.1/libdispatch/dvar.o trimmed_netcdf-4.2.1.1/libdispatch/dvarget.o trimmed_netcdf-4.2.1.1/libdispatch/dvarinq.o trimmed_netcdf-4.2.1.1/libdispatch/dvarput.o trimmed_netcdf-4.2.1.1/libdispatch/dvlen.o trimmed_netcdf-4.2.1.1/libdispatch/nc_uri.o trimmed_netcdf-4.2.1.1/libdispatch/ncaux.o trimmed_netcdf-4.2.1.1/libdispatch/ncbytes.o trimmed_netcdf-4.2.1.1/libdispatch/nchashmap.o trimmed_netcdf-4.2.1.1/libdispatch/nclist.o trimmed_netcdf-4.2.1.1/libdispatch/nctime.o trimmed_netcdf-4.2.1.1/libsrc/attr.o trimmed_netcdf-4.2.1.1/libsrc/dim.o trimmed_netcdf-4.2.1.1/libsrc/lookup3.o trimmed_netcdf-4.2.1.1/libsrc/memio.o trimmed_netcdf-4.2.1.1/libsrc/nc.o trimmed_netcdf-4.2.1.1/libsrc/nc3dispatch.o trimmed_netcdf-4.2.1.1/libsrc/ncio.o trimmed_netcdf-4.2.1.1/libsrc/nclistmgr.o trimmed_netcdf-4.2.1.1/libsrc/ncx.o trimmed_netcdf-4.2.1.1/libsrc/posixio.o trimmed_netcdf-4.2.1.1/libsrc/putget.o trimmed_netcdf-4.2.1.1/libsrc/v1hpg.o trimmed_netcdf-4.2.1.1/libsrc/var.o trimmed_netcdf-4.2.1.1/libsrc4/error4.o trimmed_netcdf-4.2.1.1/libsrc4/nc4attr.o trimmed_netcdf-4.2.1.1/libsrc4/nc4dim.o trimmed_netcdf-4.2.1.1/libsrc4/nc4dispatch.o trimmed_netcdf-4.2.1.1/libsrc4/nc4file.o trimmed_netcdf-4.2.1.1/libsrc4/nc4grp.o trimmed_netcdf-4.2.1.1/libsrc4/nc4hdf.o trimmed_netcdf-4.2.1.1/libsrc4/nc4internal.o trimmed_netcdf-4.2.1.1/libsrc4/nc4type.o trimmed_netcdf-4.2.1.1/libsrc4/nc4var.o trimmed_netcdf-4.2.1.1/libsrc4/ncfunc.o -L/usr/lib -lhdf5 -lhdf5_hl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
cp ncdfFlow.so libncdfFlow.dylib 
cp libncdfFlow.dylib ../inst/lib
rm libncdfFlow.dylib
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ncdfFlow)


>>>>>>> 
>>>>>>> FIXING LINKS FOR ncdfFlow.buildbin-libdir/ncdfFlow/libs//ncdfFlow.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "ncdfFlow.buildbin-libdir/ncdfFlow/libs//ncdfFlow.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "ncdfFlow.buildbin-libdir/ncdfFlow/libs//ncdfFlow.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "ncdfFlow.buildbin-libdir/ncdfFlow/libs//ncdfFlow.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "ncdfFlow.buildbin-libdir/ncdfFlow/libs//ncdfFlow.so"