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###
### Running command:
###
###   rm -rf GeneSelectMMD.buildbin-libdir && mkdir GeneSelectMMD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeneSelectMMD_2.44.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GeneSelectMMD.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GeneSelectMMD.buildbin-libdir GeneSelectMMD_2.44.1.tar.gz'
>>>>>>> 

* installing *source* package ‘GeneSelectMMD’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
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 GeneSelectMMD_init.c -o GeneSelectMMD_init.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c Qfunc.f -o Qfunc.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c blas.f -o blas.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 isnan.c -o isnan.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c lbfgsb.f -o lbfgsb.o
lbfgsb.f:1409:25:

 1409 |      +                 tu,tl,wmc,wmp,wmw,ddot,tj,tj0,neggi,sbgnrm,
      |                         ^
Warning: ‘tu’ may be used uninitialized [-Wmaybe-uninitialized]
lbfgsb.f:1482:72:

 1482 |                t(nbreak) = tl/(-neggi)
      |                                                                        ^
Warning: ‘tl’ may be used uninitialized [-Wmaybe-uninitialized]
lbfgsb.f:1409:28:

 1409 |      +                 tu,tl,wmc,wmp,wmw,ddot,tj,tj0,neggi,sbgnrm,
      |                            ^
note: ‘tl’ was declared here
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c lbfgsbDriver.f -o lbfgsbDriver.o
lbfgsbDriver.f:243:71:

  243 |      +                 wa(2*mmax*nmax + 5*nmax + 11*mmax*mmax + 8*mmax)
      |                                                                       1
Warning: Array ‘wa’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising]
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c linpack.f -o linpack.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c llkhFun.f -o llkhFun.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c myTtest.f -o myTtest.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c paraEstLoop.f -o paraEstLoop.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 pt.c -o pt.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c timer.f -o timer.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c wiFun.f -o wiFun.o
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 GeneSelectMMD.so GeneSelectMMD_init.o Qfunc.o blas.o isnan.o lbfgsb.o lbfgsbDriver.o linpack.o llkhFun.o myTtest.o paraEstLoop.o pt.o timer.o wiFun.o -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for _negqfunc_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for _lbfgsbdriver_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _llkhfun_: registers 78 and 79 not saved contiguously in frameld: warning: could not create compact unwind for _paraestloop_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _prn1lb_.part.0: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _prn3lb_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _myttest_: register 75 saved somewhere other than in frame
ld: warning: could not create compact unwind for _matupd_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _dnegqfunc_: registers 78 and 79 not saved contiguously in frame

ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
ld: warning: could not create compact unwind for _wifun_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for _prn2lb_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _dcsrch_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for _lnsrlb_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _subsm_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _freev_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _cauchy_: registers 74 and 75 not saved contiguously in frame
ld: warning: could not create compact unwind for _active_: registers 19 and 20 not saved contiguously in frame
ld: warning: could not create compact unwind for _mainlb_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _setulb_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _dtrsl_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _dcopy_: register 22 saved somewhere other than in frame
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GeneSelectMMD.buildbin-libdir/00LOCK-GeneSelectMMD/00new/GeneSelectMMD/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 (GeneSelectMMD)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so
>>>>>>> 

>>>>>>> Paths before fix:
GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so:
	GeneSelectMMD.so (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so"

>>>>>>> Paths after fix:

GeneSelectMMD.buildbin-libdir/GeneSelectMMD/libs/GeneSelectMMD.so:
	GeneSelectMMD.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)