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Package 355/444HostnameOS / ArchBUILDCHECKBUILD BIN
rGADEM 1.3.0
Arnaud Droit
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rGADEM
Last Changed Rev: 50295 / Revision: 53825
Last Changed Date: 2010-10-17 22:57:44 -0700 (Sun, 17 Oct 2010)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK  WARNINGS [ OK ]

Summary

Package: rGADEM
Version: 1.3.0
Command: /Users/biocbuild/BBS/utils/build-universal.sh rGADEM_1.3.0.tar.gz /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R rGADEM.buildbin-libdir
StartedAt: 2011-03-17 18:05:24 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 18:06:02 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 38.0 seconds
RetCode: 0
Status:  OK 
PackageFile: rGADEM_1.3.0.tgz
PackageFileSize: 523.8 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=rGADEM.buildbin-libdir rGADEM_1.3.0.tar.gz'
>>>>>>> 

* installing *source* package 'rGADEM' ...
checking for gcc... gcc -arch i386 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -arch i386 -std=gnu99 -E
checking for gcc -arch i386 -std=gnu99 option to support OpenMP... -fopenmp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... yes
checking dispatch/dispatch.h presence... yes
checking for dispatch/dispatch.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
config.status: src/config.h is unchanged
** 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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:123: warning: unused variable 'nsitesEM'
Gadem_Analysis.c:143: warning: 'numTopWmerInB' may be used uninitialized in this function
Gadem_Analysis.c:118: warning: 'llrCutoff' may be used uninitialized in this function
Gadem_Analysis.c:112: warning: 'empDim' may be used uninitialized in this function
Gadem_Analysis.c:109: warning: 'llrDim' may be used uninitialized in this function
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c align_sites.c -o align_sites.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c alloc.c -o alloc.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c background.c -o background.o
background.c: In function 'read_userBackgModel':
background.c:42: warning: ordered comparison of pointer with integer zero
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c base_frequency.c -o base_frequency.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c check_convergence.c -o check_convergence.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c check_pwm_dist.c -o check_pwm_dist.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c consensus.c -o consensus.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c construct_pwm.c -o construct_pwm.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c copy_pwm.c -o copy_pwm.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c crossover.c -o crossover.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c effect_seq_len.c -o effect_seq_len.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c evalue_meme.c -o evalue_meme.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c extend_alignment.c -o extend_alignment.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c initial_population.c -o initial_population.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c mask_sites.c -o mask_sites.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c mutation.c -o mutation.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c normalization.c -o normalization.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c output.c -o output.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c pwm_score_distr.c -o pwm_score_distr.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c read_matrix.c -o read_matrix.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c read_pwm0.c -o read_pwm0.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c read_seq.c -o read_seq.o
read_seq.c: In function 'read_seq':
read_seq.c:34: warning: ordered comparison of pointer with integer zero
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c reverse_seq.c -o reverse_seq.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c sample_wo_replacement.c -o sample_wo_replacement.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c scan_sites.c -o scan_sites.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c score_subsequence.c -o score_subsequence.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c selection.c -o selection.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c sort.c -o sort.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c top_kmers.c -o top_kmers.o
top_kmers.c: In function 'top_kmer':
top_kmers.c:154: warning: 'numAvailableTopKmer' may be used uninitialized in this function
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c transform_pwm.c -o transform_pwm.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c weights.c -o weights.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o rGADEM.so Gadem_Analysis.o align_sites.o alloc.o background.o base_frequency.o check_convergence.o check_pwm_dist.o consensus.o construct_pwm.o copy_pwm.o crossover.o effect_seq_len.o evalue_meme.o extend_alignment.o initial_population.o mask_sites.o mutation.o normalization.o output.o pwm_score_distr.o read_matrix.o read_pwm0.o read_seq.o reverse_seq.o sample_wo_replacement.o scan_sites.o score_subsequence.o selection.o sort.o top_kmers.o transform_pwm.o weights.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/rGADEM.buildbin-libdir/rGADEM/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: grid
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (rGADEM)


>>>>>>> 
>>>>>>> FIXING LINKS FOR rGADEM.buildbin-libdir/rGADEM/libs/i386/rGADEM.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" "rGADEM.buildbin-libdir/rGADEM/libs/i386/rGADEM.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "rGADEM.buildbin-libdir/rGADEM/libs/i386/rGADEM.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" "rGADEM.buildbin-libdir/rGADEM/libs/i386/rGADEM.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "rGADEM.buildbin-libdir/rGADEM/libs/i386/rGADEM.so"


>>>>>>> 
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=rGADEM.buildbin-libdir --libs-only rGADEM_1.3.0.tar.gz'
>>>>>>> 

* installing *source* package 'rGADEM' ...
checking for gcc... gcc -arch ppc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch ppc -std=gnu99 accepts -g... yes
checking for gcc -arch ppc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -arch ppc -std=gnu99 -E
checking for gcc -arch ppc -std=gnu99 option to support OpenMP... -fopenmp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... yes
checking dispatch/dispatch.h presence... yes
checking for dispatch/dispatch.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
config.status: src/config.h is unchanged
** libs
*** 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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:123: warning: unused variable 'nsitesEM'
Gadem_Analysis.c:143: warning: 'numTopWmerInB' may be used uninitialized in this function
Gadem_Analysis.c:118: warning: 'llrCutoff' may be used uninitialized in this function
Gadem_Analysis.c:112: warning: 'empDim' may be used uninitialized in this function
Gadem_Analysis.c:109: warning: 'llrDim' may be used uninitialized in this function
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c align_sites.c -o align_sites.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c alloc.c -o alloc.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c background.c -o background.o
background.c: In function 'read_userBackgModel':
background.c:42: warning: ordered comparison of pointer with integer zero
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c base_frequency.c -o base_frequency.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c check_convergence.c -o check_convergence.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c check_pwm_dist.c -o check_pwm_dist.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c consensus.c -o consensus.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c construct_pwm.c -o construct_pwm.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c copy_pwm.c -o copy_pwm.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c crossover.c -o crossover.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c effect_seq_len.c -o effect_seq_len.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c evalue_meme.c -o evalue_meme.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c extend_alignment.c -o extend_alignment.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c initial_population.c -o initial_population.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c mask_sites.c -o mask_sites.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c mutation.c -o mutation.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c normalization.c -o normalization.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c output.c -o output.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c pwm_score_distr.c -o pwm_score_distr.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c read_matrix.c -o read_matrix.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c read_pwm0.c -o read_pwm0.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c read_seq.c -o read_seq.o
read_seq.c: In function 'read_seq':
read_seq.c:34: warning: ordered comparison of pointer with integer zero
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c reverse_seq.c -o reverse_seq.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c sample_wo_replacement.c -o sample_wo_replacement.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c scan_sites.c -o scan_sites.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c score_subsequence.c -o score_subsequence.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c selection.c -o selection.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c sort.c -o sort.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c top_kmers.c -o top_kmers.o
top_kmers.c: In function 'top_kmer':
top_kmers.c:154: warning: 'numAvailableTopKmer' may be used uninitialized in this function
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c transform_pwm.c -o transform_pwm.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c weights.c -o weights.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o rGADEM.so Gadem_Analysis.o align_sites.o alloc.o background.o base_frequency.o check_convergence.o check_pwm_dist.o consensus.o construct_pwm.o copy_pwm.o crossover.o effect_seq_len.o evalue_meme.o extend_alignment.o initial_population.o mask_sites.o mutation.o normalization.o output.o pwm_score_distr.o read_matrix.o read_pwm0.o read_seq.o reverse_seq.o sample_wo_replacement.o scan_sites.o score_subsequence.o selection.o sort.o top_kmers.o transform_pwm.o weights.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/ppc

* DONE (rGADEM)


>>>>>>> 
>>>>>>> FIXING LINKS FOR rGADEM.buildbin-libdir/rGADEM/libs/ppc/rGADEM.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" "rGADEM.buildbin-libdir/rGADEM/libs/ppc/rGADEM.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "rGADEM.buildbin-libdir/rGADEM/libs/ppc/rGADEM.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" "rGADEM.buildbin-libdir/rGADEM/libs/ppc/rGADEM.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "rGADEM.buildbin-libdir/rGADEM/libs/ppc/rGADEM.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --library=rGADEM.buildbin-libdir --libs-only rGADEM_1.3.0.tar.gz'
>>>>>>> 

* installing *source* package 'rGADEM' ...
checking for gcc... gcc -arch x86_64 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch x86_64 -std=gnu99 accepts -g... yes
checking for gcc -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -arch x86_64 -std=gnu99 -E
checking for gcc -arch x86_64 -std=gnu99 option to support OpenMP... -fopenmp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... yes
checking dispatch/dispatch.h presence... yes
checking for dispatch/dispatch.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
config.status: src/config.h is unchanged
** libs
*** 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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:123: warning: unused variable 'nsitesEM'
Gadem_Analysis.c:143: warning: 'numTopWmerInB' may be used uninitialized in this function
Gadem_Analysis.c:118: warning: 'llrCutoff' may be used uninitialized in this function
Gadem_Analysis.c:112: warning: 'empDim' may be used uninitialized in this function
Gadem_Analysis.c:109: warning: 'llrDim' may be used uninitialized in this function
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c align_sites.c -o align_sites.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c alloc.c -o alloc.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c background.c -o background.o
background.c: In function 'read_userBackgModel':
background.c:42: warning: ordered comparison of pointer with integer zero
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c base_frequency.c -o base_frequency.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c check_convergence.c -o check_convergence.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c check_pwm_dist.c -o check_pwm_dist.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c consensus.c -o consensus.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c construct_pwm.c -o construct_pwm.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c copy_pwm.c -o copy_pwm.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c crossover.c -o crossover.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c effect_seq_len.c -o effect_seq_len.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c evalue_meme.c -o evalue_meme.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c extend_alignment.c -o extend_alignment.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c initial_population.c -o initial_population.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c mask_sites.c -o mask_sites.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c mutation.c -o mutation.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c normalization.c -o normalization.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c output.c -o output.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c pwm_score_distr.c -o pwm_score_distr.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c read_matrix.c -o read_matrix.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c read_pwm0.c -o read_pwm0.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c read_seq.c -o read_seq.o
read_seq.c: In function 'read_seq':
read_seq.c:34: warning: ordered comparison of pointer with integer zero
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c reverse_seq.c -o reverse_seq.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c sample_wo_replacement.c -o sample_wo_replacement.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c scan_sites.c -o scan_sites.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c score_subsequence.c -o score_subsequence.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c selection.c -o selection.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c sort.c -o sort.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c top_kmers.c -o top_kmers.o
top_kmers.c: In function 'top_kmer':
top_kmers.c:154: warning: 'numAvailableTopKmer' may be used uninitialized in this function
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c transform_pwm.c -o transform_pwm.o
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   -fopenmp -fPIC  -g -O2 -Wall -pedantic -c weights.c -o weights.o
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 rGADEM.so Gadem_Analysis.o align_sites.o alloc.o background.o base_frequency.o check_convergence.o check_pwm_dist.o consensus.o construct_pwm.o copy_pwm.o crossover.o effect_seq_len.o evalue_meme.o extend_alignment.o initial_population.o mask_sites.o mutation.o normalization.o output.o pwm_score_distr.o read_matrix.o read_pwm0.o read_seq.o reverse_seq.o sample_wo_replacement.o scan_sites.o score_subsequence.o selection.o sort.o top_kmers.o transform_pwm.o weights.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/x86_64

* DONE (rGADEM)


>>>>>>> 
>>>>>>> FIXING LINKS FOR rGADEM.buildbin-libdir/rGADEM/libs/x86_64/rGADEM.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" "rGADEM.buildbin-libdir/rGADEM/libs/x86_64/rGADEM.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "rGADEM.buildbin-libdir/rGADEM/libs/x86_64/rGADEM.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" "rGADEM.buildbin-libdir/rGADEM/libs/x86_64/rGADEM.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "rGADEM.buildbin-libdir/rGADEM/libs/x86_64/rGADEM.so"