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###
### Running command:
###
### rm -rf BiRewire.buildbin-libdir && mkdir BiRewire.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiRewire_3.36.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BiRewire.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BiRewire.buildbin-libdir BiRewire_3.36.0.tar.gz'
>>>>>>>
* installing *source* package ‘BiRewire’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BiRewire.c -o BiRewire.o
BiRewire.c:149:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:221:37: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:229:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:280:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:332:37: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:339:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:402:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:454:37: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:461:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:588:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:652:37: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:737:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:844:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:893:37: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:962:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:1096:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:1144:37: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
BiRewire.c:1183:35: warning: format specifies type 'int' but the argument has type 'time_t' (aka 'long') [-Wformat]
Rprintf("DONE in %d seconds \n",-(tin-tfin));
~~ ^~~~~~~~~~~
%ld
18 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 interface.c -o interface.o
interface.c:28:23: warning: variable 'e' set but not used [-Wunused-but-set-variable]
size_t i,dim,nc,nr,j,e=0;
^
interface.c:105:68: warning: data argument not used by format string [-Wformat-extra-args]
warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:877:20: note: expanded from macro 'asInteger'
#define asInteger Rf_asInteger
^
interface.c:147:68: warning: data argument not used by format string [-Wformat-extra-args]
warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:877:20: note: expanded from macro 'asInteger'
#define asInteger Rf_asInteger
^
interface.c:167:23: warning: variable 'e' set but not used [-Wunused-but-set-variable]
size_t i,dim,nc,nr,j,e=0;
^
interface.c:252:68: warning: data argument not used by format string [-Wformat-extra-args]
warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:877:20: note: expanded from macro 'asInteger'
#define asInteger Rf_asInteger
^
interface.c:296:68: warning: data argument not used by format string [-Wformat-extra-args]
warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:877:20: note: expanded from macro 'asInteger'
#define asInteger Rf_asInteger
^
6 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BiRewire.so BiRewire.o interface.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/BiRewire.buildbin-libdir/00LOCK-BiRewire/00new/BiRewire/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
** 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 (BiRewire)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR BiRewire.buildbin-libdir/BiRewire/libs/BiRewire.so
>>>>>>>
>>>>>>> Paths before fix:
BiRewire.buildbin-libdir/BiRewire/libs/BiRewire.so:
BiRewire.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "BiRewire.buildbin-libdir/BiRewire/libs/BiRewire.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "BiRewire.buildbin-libdir/BiRewire/libs/BiRewire.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "BiRewire.buildbin-libdir/BiRewire/libs/BiRewire.so"
>>>>>>> Paths after fix:
BiRewire.buildbin-libdir/BiRewire/libs/BiRewire.so:
BiRewire.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
