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###
### Running command:
###
### rm -rf rama.buildbin-libdir && mkdir rama.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rama_1.72.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rama.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rama.buildbin-libdir rama_1.72.0.tar.gz'
>>>>>>>
* installing *source* package ‘rama’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c estimation_slice.c -o estimation_slice.o
estimation_slice.c:116:24: warning: unused variable 'SS12' [-Wunused-variable]
double SSR1=0,SSR2=0,SS12=0;
^
estimation_slice.c:117:10: warning: unused variable 'pi' [-Wunused-variable]
double pi=3.14;
^
estimation_slice.c:113:10: warning: unused variable 'lambda_eps1_new' [-Wunused-variable]
double lambda_eps1_new, lambda_eps2_new;
^
estimation_slice.c:122:10: warning: unused variable 'SSeps_sd_new' [-Wunused-variable]
double SSeps_sd_new=0.;
^
estimation_slice.c:114:10: warning: unused variable 'l_epsilon' [-Wunused-variable]
double l_epsilon=0,l_epsilon_new=0;
^
estimation_slice.c:121:10: warning: unused variable 'SSeps_sd' [-Wunused-variable]
double SSeps_sd=0.;
^
estimation_slice.c:113:27: warning: unused variable 'lambda_eps2_new' [-Wunused-variable]
double lambda_eps1_new, lambda_eps2_new;
^
estimation_slice.c:114:22: warning: unused variable 'l_epsilon_new' [-Wunused-variable]
double l_epsilon=0,l_epsilon_new=0;
^
estimation_slice.c:115:10: warning: unused variable 'dens_epsilon' [-Wunused-variable]
double dens_epsilon=0,dens_epsilon_new=0;
^
estimation_slice.c:116:10: warning: unused variable 'SSR1' [-Wunused-variable]
double SSR1=0,SSR2=0,SS12=0;
^
estimation_slice.c:115:25: warning: unused variable 'dens_epsilon_new' [-Wunused-variable]
double dens_epsilon=0,dens_epsilon_new=0;
^
estimation_slice.c:134:24: warning: variable 'mean_gamma2' set but not used [-Wunused-but-set-variable]
double mean_gamma1=0,mean_gamma2=0;
^
estimation_slice.c:116:17: warning: unused variable 'SSR2' [-Wunused-variable]
double SSR1=0,SSR2=0,SS12=0;
^
estimation_slice.c:134:10: warning: variable 'mean_gamma1' set but not used [-Wunused-but-set-variable]
double mean_gamma1=0,mean_gamma2=0;
^
14 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ex_estimation_slice.c -o ex_estimation_slice.o
ex_estimation_slice.c:119:10: warning: unused variable 'dens_t' [-Wunused-variable]
double dens_t=0,dens_t_new=0;
^
ex_estimation_slice.c:119:19: warning: unused variable 'dens_t_new' [-Wunused-variable]
double dens_t=0,dens_t_new=0;
^
ex_estimation_slice.c:129:24: warning: variable 'mean_gamma2' set but not used [-Wunused-but-set-variable]
double mean_gamma1=0,mean_gamma2=0;
^
ex_estimation_slice.c:129:10: warning: variable 'mean_gamma1' set but not used [-Wunused-but-set-variable]
double mean_gamma1=0,mean_gamma2=0;
^
ex_estimation_slice.c:144:10: warning: unused variable 'old_a' [-Wunused-variable]
double old_a=0,width_a=1.;
^
ex_estimation_slice.c:143:10: warning: unused variable 'old_b' [-Wunused-variable]
double old_b=0,width_b=5.;
^
ex_estimation_slice.c:112:10: warning: unused variable 'pi' [-Wunused-variable]
double pi=3.14;
^
ex_estimation_slice.c:137:10: warning: unused variable 'sum_res1' [-Wunused-variable]
double sum_res1;
^
ex_estimation_slice.c:138:10: warning: unused variable 'sum_res2' [-Wunused-variable]
double sum_res2;
^
9 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mean.sd.c -o mean.sd.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c reorder.c -o reorder.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.c -o util.o
util.c:574:11: warning: unused variable 'k' [-Wunused-variable]
int i,j,k;
^
util.c:629:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
~~~~^
util.c:629:13: note: place parentheses around the '>' expression to silence this warning
while(K>0 & (z<log_f_L | z<log_f_R))
^
( )
util.c:629:13: note: place parentheses around the & expression to evaluate it first
while(K>0 & (z<log_f_L | z<log_f_R))
^
( )
util.c:613:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, a1;
^
util.c:703:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
~~~~^
util.c:703:13: note: place parentheses around the '>' expression to silence this warning
while(K>0 & (z<log_f_L | z<log_f_R))
^
( )
util.c:703:13: note: place parentheses around the & expression to evaluate it first
while(K>0 & (z<log_f_L | z<log_f_R))
^
( )
util.c:686:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, b1;
^
util.c:876:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
~~~~^
util.c:876:13: note: place parentheses around the '>' expression to silence this warning
while(K>0 & (z<log_f_L | z<log_f_R))
^
( )
util.c:876:13: note: place parentheses around the & expression to evaluate it first
while(K>0 & (z<log_f_L | z<log_f_R))
^
( )
util.c:860:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, rho_new;
^
util.c:1019:13: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses]
while(K>0 & (z<log_f_L | z<log_f_R))
~~~~^
util.c:1019:13: note: place parentheses around the '>' expression to silence this warning
while(K>0 & (z<log_f_L | z<log_f_R))
^
( )
util.c:1019:13: note: place parentheses around the & expression to evaluate it first
while(K>0 & (z<log_f_L | z<log_f_R))
^
( )
util.c:1000:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, shift_new;
^
util.c:1082:13: warning: unused variable 'v' [-Wunused-variable]
double u, v, L, R, z, shift_new;
^
10 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o rama.so estimation_slice.o ex_estimation_slice.o mean.sd.o reorder.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/rama.buildbin-libdir/00LOCK-rama/00new/rama/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'rama' is deprecated and will be removed from Bioconductor
version 3.17
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'rama' is deprecated and will be removed from Bioconductor
version 3.17
** testing if installed package keeps a record of temporary installation path
* DONE (rama)
>>>>>>>
>>>>>>> FIXING LINKS FOR rama.buildbin-libdir/rama/libs/rama.so
>>>>>>>
install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "rama.buildbin-libdir/rama/libs/rama.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "rama.buildbin-libdir/rama/libs/rama.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "rama.buildbin-libdir/rama/libs/rama.so"
