BioC 3.2: BUILD BIN report for rGADEM on perceval

Package: rGADEM

Version: 2.18.0

Command: rm -rf rGADEM.buildbin-libdir && mkdir rGADEM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rGADEM_2.18.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R rGADEM.buildbin-libdir

StartedAt: 2015-11-10 11:42:20 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 11:42:47 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 26.9 seconds

RetCode: 0

Status:  OK

PackageFile: rGADEM_2.18.0.tgz

PackageFileSize: 378.1 KiB

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### Running command:
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###   rm -rf rGADEM.buildbin-libdir && mkdir rGADEM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rGADEM_2.18.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R rGADEM.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rGADEM.buildbin-libdir rGADEM_2.18.0.tar.gz'
>>>>>>> 

* installing *source* package ‘rGADEM’ ...
checking for gcc... llvm-gcc-4.2 -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 llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E
checking for llvm-gcc-4.2 -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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c Gadem_Analysis.c -o Gadem_Analysis.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c align_sites.c -o align_sites.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c alloc.c -o alloc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c background.c -o background.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c base_frequency.c -o base_frequency.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c check_convergence.c -o check_convergence.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c check_pwm_dist.c -o check_pwm_dist.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c consensus.c -o consensus.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c construct_pwm.c -o construct_pwm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c copy_pwm.c -o copy_pwm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c crossover.c -o crossover.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c effect_seq_len.c -o effect_seq_len.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c evalue_meme.c -o evalue_meme.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c extend_alignment.c -o extend_alignment.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c initial_population.c -o initial_population.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c mask_sites.c -o mask_sites.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c mutation.c -o mutation.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c normalization.c -o normalization.o
normalization.c: In function ‘range’:
normalization.c:124: warning: implicit declaration of function ‘Rprintf’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c output.c -o output.o
output.c: In function ‘print_bed’:
output.c:11: warning: unused variable ‘f1’
output.c: In function ‘print_result_R’:
output.c:326: warning: unused variable ‘number’
output.c:324: warning: unused variable ‘base’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c pwm_score_distr.c -o pwm_score_distr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c read_matrix.c -o read_matrix.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c read_pwm0.c -o read_pwm0.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c read_seq.c -o read_seq.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c reverse_seq.c -o reverse_seq.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c sample_wo_replacement.c -o sample_wo_replacement.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c scan_sites.c -o scan_sites.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c score_subsequence.c -o score_subsequence.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c selection.c -o selection.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c sort.c -o sort.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c top_kmers.c -o top_kmers.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c transform_pwm.c -o transform_pwm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -fPIC  -mtune=core2 -g -O2 -Wall  -c weights.c -o weights.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/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -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-3.2-bioc/meat/rGADEM.buildbin-libdir/rGADEM/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 (rGADEM)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "rGADEM.buildbin-libdir/rGADEM/libs//rGADEM.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "rGADEM.buildbin-libdir/rGADEM/libs//rGADEM.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "rGADEM.buildbin-libdir/rGADEM/libs//rGADEM.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "rGADEM.buildbin-libdir/rGADEM/libs//rGADEM.so"