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###
### Running command:
###
### rm -rf CBN2Path.buildbin-libdir && mkdir CBN2Path.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CBN2Path_0.99.17.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CBN2Path.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CBN2Path.buildbin-libdir CBN2Path_0.99.17.tar.gz'
>>>>>>>
* installing *source* package ‘CBN2Path’ ...
** this is package ‘CBN2Path’ version ‘0.99.17’
** using staged installation
checking for gcc... clang -arch x86_64
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 the compiler supports GNU C... yes
checking whether clang -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to enable C11 features... none needed
checking for gsl-config... /usr/local/bin/gsl-config
checking if GSL version >= 2.5... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bcbn.c -o bcbn.o
bcbn.c:433:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
bcbn.c:554:36: warning: if statement has empty body [-Wempty-body]
if(fscanf(input, "%d %d", N, &p));
^
bcbn.c:554:36: note: put the semicolon on a separate line to silence this warning
bcbn.c:611:30: warning: if statement has empty body [-Wempty-body]
if(fscanf(input, "%d", &n));
^
bcbn.c:611:30: note: put the semicolon on a separate line to silence this warning
bcbn.c:623:43: warning: if statement has empty body [-Wempty-body]
if(fscanf(input,"%d %d", &left, &right));
^
bcbn.c:623:43: note: put the semicolon on a separate line to silence this warning
bcbn.c:633:45: warning: if statement has empty body [-Wempty-body]
if(fscanf(input,"%d %d", &left, &right));
^
bcbn.c:633:45: note: put the semicolon on a separate line to silence this warning
bcbn.c:641:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
bcbn.c:931:30: warning: if statement has empty body [-Wempty-body]
if(fscanf(input, "%d", &n));
^
bcbn.c:931:30: note: put the semicolon on a separate line to silence this warning
bcbn.c:943:43: warning: if statement has empty body [-Wempty-body]
if(fscanf(input,"%d %d", &left, &right));
^
bcbn.c:943:43: note: put the semicolon on a separate line to silence this warning
bcbn.c:953:45: warning: if statement has empty body [-Wempty-body]
if(fscanf(input,"%d %d", &left, &right));
^
bcbn.c:953:45: note: put the semicolon on a separate line to silence this warning
bcbn.c:1075:10: warning: variable 'p' set but not used [-Wunused-but-set-variable]
double p = 0;
^
bcbn.c:1056:13: warning: unused variable 'k' [-Wunused-variable]
int i,j,c,k;
^
bcbn.c:1056:9: warning: unused variable 'j' [-Wunused-variable]
int i,j,c,k;
^
bcbn.c:1281:15: warning: unused variable 'likelihood' [-Wunused-variable]
long double likelihood, likelihood_d;
^
bcbn.c:1367:25: warning: variable 'x' set but not used [-Wunused-but-set-variable]
double alpha,beta,var,x;
^
bcbn.c:1367:21: warning: unused variable 'var' [-Wunused-variable]
double alpha,beta,var,x;
^
bcbn.c:1380:21: warning: unused variable 'var' [-Wunused-variable]
double alpha,beta,var,x;
^
bcbn.c:1380:25: warning: variable 'x' set but not used [-Wunused-but-set-variable]
double alpha,beta,var,x;
^
bcbn.c:1449:11: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,N_compatible,N_all_comp;
^
bcbn.c:1550:22: warning: unused variable 'N_compatible' [-Wunused-variable]
int i,j,N_all_comp,N_compatible,k;
^
bcbn.c:1550:11: warning: variable 'N_all_comp' set but not used [-Wunused-but-set-variable]
int i,j,N_all_comp,N_compatible,k;
^
bcbn.c:1550:35: warning: unused variable 'k' [-Wunused-variable]
int i,j,N_all_comp,N_compatible,k;
^
bcbn.c:1675:25: warning: unused variable 'x' [-Wunused-variable]
double alpha,beta,var,x;
^
bcbn.c:1675:10: warning: unused variable 'alpha' [-Wunused-variable]
double alpha,beta,var,x;
^
bcbn.c:1675:16: warning: unused variable 'beta' [-Wunused-variable]
double alpha,beta,var,x;
^
bcbn.c:1675:21: warning: unused variable 'var' [-Wunused-variable]
double alpha,beta,var,x;
^
bcbn.c:1755:11: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,N_compatible,N_all_comp;
^
bcbn.c:1878:11: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,N_compatible,N_all_comp;
^
bcbn.c:1878:26: warning: variable 'N_all_comp' set but not used [-Wunused-but-set-variable]
int i,j,k,N_compatible,N_all_comp;
^
bcbn.c:1878:13: warning: unused variable 'N_compatible' [-Wunused-variable]
int i,j,k,N_compatible,N_all_comp;
^
bcbn.c:1946:26: warning: variable 'N_all_comp' set but not used [-Wunused-but-set-variable]
int i,j,k,N_compatible,N_all_comp;
^
bcbn.c:1957:7: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
bcbn.c:1946:11: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,N_compatible,N_all_comp;
^
bcbn.c:1946:13: warning: unused variable 'N_compatible' [-Wunused-variable]
int i,j,k,N_compatible,N_all_comp;
^
bcbn.c:1997:11: warning: unused variable 'k' [-Wunused-variable]
int i,j,k,N_compatible,N_all_comp;
^
bcbn.c:1997:13: warning: unused variable 'N_compatible' [-Wunused-variable]
int i,j,k,N_compatible,N_all_comp;
^
bcbn.c:1997:26: warning: variable 'N_all_comp' set but not used [-Wunused-but-set-variable]
int i,j,k,N_compatible,N_all_comp;
^
bcbn.c:2008:7: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
bcbn.c:2358:7: warning: unused variable 'i' [-Wunused-variable]
int i,j,k = 0;
^
bcbn.c:2358:9: warning: unused variable 'j' [-Wunused-variable]
int i,j,k = 0;
^
bcbn.c:2362:7: warning: unused variable 'accepted' [-Wunused-variable]
int accepted = 0;
^
bcbn.c:2620:22: warning: unused variable 'MH_ratio' [-Wunused-variable]
long double alpha, MH_ratio;
^
41 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ctcbn.c -o ctcbn.o
In file included from ctcbn.c:3:
./ct-cbn.h:184:7: warning: unused variable 'j' [-Wunused-variable]
int j;
^
./ct-cbn.h:551:36: warning: if statement has empty body [-Wempty-body]
if(fscanf(input, "%d %d", N, &p));
^
./ct-cbn.h:551:36: note: put the semicolon on a separate line to silence this warning
./ct-cbn.h:611:36: warning: if statement has empty body [-Wempty-body]
if(fscanf(input, "%d %d", N, &p));
^
./ct-cbn.h:611:36: note: put the semicolon on a separate line to silence this warning
./ct-cbn.h:670:30: warning: if statement has empty body [-Wempty-body]
if(fscanf(input, "%d", &n));
^
./ct-cbn.h:670:30: note: put the semicolon on a separate line to silence this warning
./ct-cbn.h:682:43: warning: if statement has empty body [-Wempty-body]
if(fscanf(input,"%d %d", &left, &right));
^
./ct-cbn.h:682:43: note: put the semicolon on a separate line to silence this warning
./ct-cbn.h:692:45: warning: if statement has empty body [-Wempty-body]
if(fscanf(input,"%d %d", &left, &right));
^
./ct-cbn.h:692:45: note: put the semicolon on a separate line to silence this warning
./ct-cbn.h:719:33: warning: if statement has empty body [-Wempty-body]
if(fscanf(input, "%lf", &x));
^
./ct-cbn.h:719:33: note: put the semicolon on a separate line to silence this warning
./ct-cbn.h:803:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
./ct-cbn.h:2721:17: warning: variable 'alpha_new' set but not used [-Wunused-but-set-variable]
double alpha, alpha_new;
^
./ct-cbn.h:3305:7: warning: variable 'mut_next' set but not used [-Wunused-but-set-variable]
int mut_next, index_next;
^
ctcbn.c:88:7: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
ctcbn.c:79:7: warning: unused variable 'verbose' [-Wunused-variable]
int verbose = 0;
^
ctcbn.c:84:7: warning: unused variable 'GPS' [-Wunused-variable]
int GPS = 0;
^
ctcbn.c:303:7: warning: unused variable 'f_flag' [-Wunused-variable]
int f_flag = 0;
^
ctcbn.c:314:7: warning: variable 'N_iter' set but not used [-Wunused-but-set-variable]
int N_iter = 0;
^
ctcbn.c:302:7: warning: unused variable 'error_flag' [-Wunused-variable]
int error_flag = 0;
^
ctcbn.c:313:10: warning: unused variable 'T' [-Wunused-variable]
double T = REAL(temp)[0];
^
ctcbn.c:304:7: warning: variable 'e_flag' set but not used [-Wunused-but-set-variable]
int e_flag = 0;
^
ctcbn.c:306:7: warning: unused variable 'l_flag' [-Wunused-variable]
int l_flag = 0;
^
ctcbn.c:305:7: warning: unused variable 'gps_flag' [-Wunused-variable]
int gps_flag = 0;
^
ctcbn.c:308:7: warning: unused variable 't_flag' [-Wunused-variable]
int t_flag = 1;
^
ctcbn.c:319:7: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
22 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c queue.c -o queue.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o CBN2Path.so bcbn.o ctcbn.o init.o queue.o -L/usr/local/lib -lgsl -lgslcblas -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc/meat/CBN2Path.buildbin-libdir/00LOCK-CBN2Path/00new/CBN2Path/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CBN2Path)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR CBN2Path.buildbin-libdir/CBN2Path/libs/CBN2Path.so
>>>>>>>
>>>>>>> Paths before fix:
CBN2Path.buildbin-libdir/CBN2Path/libs/CBN2Path.so:
CBN2Path.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "CBN2Path.buildbin-libdir/CBN2Path/libs/CBN2Path.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "CBN2Path.buildbin-libdir/CBN2Path/libs/CBN2Path.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "CBN2Path.buildbin-libdir/CBN2Path/libs/CBN2Path.so"
>>>>>>> Paths after fix:
CBN2Path.buildbin-libdir/CBN2Path/libs/CBN2Path.so:
CBN2Path.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
