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###
### Running command:
###
###   rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNAcopy_1.74.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DNAcopy.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DNAcopy.buildbin-libdir DNAcopy_1.74.1.tar.gz'
>>>>>>> 

* installing *source* package ‘DNAcopy’ ...
** 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’
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f:283:72:

  283 |       iseg(2) = tmaxj
      |                                                                        ^
Warning: ‘tmaxj’ may be used uninitialized [-Wmaybe-uninitialized]
cbsWtstats.f:17:23:

   17 |      2     tmaxi, tmaxj, nal0
      |                       ^
note: ‘tmaxj’ was declared here
cbsWtstats.f:282:72:

  282 |       iseg(1) = tmaxi
      |                                                                        ^
Warning: ‘tmaxi’ may be used uninitialized [-Wmaybe-uninitialized]
cbsWtstats.f:17:16:

   17 |      2     tmaxi, tmaxj, nal0
      |                ^
note: ‘tmaxi’ was declared here
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c cbststats.f -o cbststats.o
cbststats.f:11:63:

   11 |      1     nb2, bi, bj, ilo, ihi, jlo, jhi, alenmax, i2j, sxmxi,
      |                                                               ^
Warning: ‘sxmxi’ may be used uninitialized [-Wmaybe-uninitialized]
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c changepoints-wtd.f -o changepoints-wtd.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c changepoints.f -o changepoints.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c esegment.f -o esegment.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 flchoose.c -o flchoose.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 fphyper.c -o fphyper.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 fpnorm.c -o fpnorm.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c getbdry.f -o getbdry.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c prune.f -o prune.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 rshared.c -o rshared.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c segmentp.f -o segmentp.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c smoothCNA.f -o smoothCNA.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c tailprobs.f -o tailprobs.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 DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.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 _tpermp_: registers 74 and 75 not saved contiguously in frame
ld: warning: could not create compact unwind for _fndcpt_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _etabdry_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _getbdry_: register 77 saved somewhere other than in frame
ld: warning: could not create compact unwind for _smoothlr_: register 75 saved somewhere other than in frame
ld: warning: could not create compact unwind for _wtmaxo_: registers 74 and 75 not saved contiguously in frame
ld: warning: could not create compact unwind for _wtmaxp_: register 77 saved somewhere other than in frame
ld: warning: could not create compact unwind for _hwtmaxp_: register 75 saved somewhere other than in frame
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
ld: warning: ld: warning: could not create compact unwind for _nu_: register 77 saved somewhere other than in frame
ld: warning: could not create compact unwind for _tailp_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for _tmaxo_: register 77 saved somewhere other than in frame
ld: warning: could not create compact unwind for _tmaxp_: register 75 saved somewhere other than in frame
ld: warning: could not create compact unwind for _htmaxp_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _prune_: registers 27 and 28 not saved contiguously in frame
could not create compact unwind for _wtpermp_: register 77 saved somewhere other than in frame
ld: warning: could not create compact unwind for _wfindcpt_: register 73 saved somewhere other than in frame
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DNAcopy.buildbin-libdir/00LOCK-DNAcopy/00new/DNAcopy/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** 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 (DNAcopy)


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

>>>>>>> Paths before fix:
DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so:
	DNAcopy.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" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.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" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.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" "DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so"

>>>>>>> Paths after fix:

DNAcopy.buildbin-libdir/DNAcopy/libs/DNAcopy.so:
	DNAcopy.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)