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###
### Running command:
###
###   rm -rf gaga.buildbin-libdir && mkdir gaga.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gaga_2.57.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gaga.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gaga.buildbin-libdir gaga_2.57.0.tar.gz'
>>>>>>> 

* installing *source* package ‘gaga’ ...
** this is package ‘gaga’ version ‘2.57.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cseqdesma.c -o cseqdesma.o
cseqdesma.c:4515:14: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
 4515 | if ((*usesumx==0)) {                                               //if suff stat not pre-computed
      |      ~~~~~~~~^~~
cseqdesma.c:4515:14: note: remove extraneous parentheses around the comparison to silence this warning
 4515 | if ((*usesumx==0)) {                                               //if suff stat not pre-computed
      |     ~        ^  ~
cseqdesma.c:4515:14: note: use '=' to turn this equality comparison into an assignment
 4515 | if ((*usesumx==0)) {                                               //if suff stat not pre-computed
      |              ^~
      |              =
cseqdesma.c:5780:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
 5780 |   if ((*usel==0)) {
      |        ~~~~~^~~
cseqdesma.c:5780:13: note: remove extraneous parentheses around the comparison to silence this warning
 5780 |   if ((*usel==0)) {
      |       ~     ^  ~
cseqdesma.c:5780:13: note: use '=' to turn this equality comparison into an assignment
 5780 |   if ((*usel==0)) {
      |             ^~
      |             =
cseqdesma.c:6014:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
 6014 |   if ((*usel==0)) {
      |        ~~~~~^~~
cseqdesma.c:6014:13: note: remove extraneous parentheses around the comparison to silence this warning
 6014 |   if ((*usel==0)) {
      |       ~     ^  ~
cseqdesma.c:6014:13: note: use '=' to turn this equality comparison into an assignment
 6014 |   if ((*usel==0)) {
      |             ^~
      |             =
cseqdesma.c:6284:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
 6284 |   if ((*usel==0)) {                                           //If l values have to be generated
      |        ~~~~~^~~
cseqdesma.c:6284:13: note: remove extraneous parentheses around the comparison to silence this warning
 6284 |   if ((*usel==0)) {                                           //If l values have to be generated
      |       ~     ^  ~
cseqdesma.c:6284:13: note: use '=' to turn this equality comparison into an assignment
 6284 |   if ((*usel==0)) {                                           //If l values have to be generated
      |             ^~
      |             =
4 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cstat.c -o cstat.o
cstat.c:1836:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
 1836 |   if(abs(ndf - 2.0) < eps) {   /* df ~= 2 */
      |      ^
cstat.c:1836:6: note: use function 'fabs' instead
 1836 |   if(abs(ndf - 2.0) < eps) {   /* df ~= 2 */
      |      ^~~
      |      fabs
cstat.c:18:19: warning: unused variable 'interface_c_sccs_id' [-Wunused-const-variable]
   18 | static const char interface_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~~~~~~
cstat.c:19:19: warning: unused variable 'mess_c_sccs_id' [-Wunused-const-variable]
   19 | static const char mess_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~
cstat.c:20:19: warning: unused variable 'nrutil_c_sccs_id' [-Wunused-const-variable]
   20 | static const char nrutil_c_sccs_id[] = "%W%"; 
      |                   ^~~~~~~~~~~~~~~~
cstat.c:21:19: warning: unused variable 'vector_c_sccs_id' [-Wunused-const-variable]
   21 | static const char vector_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~~~
cstat.c:22:19: warning: unused variable 'css_c_sccs_id' [-Wunused-const-variable]
   22 | static const char css_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
      |                   ^~~~~~~~~~~~~
6 warnings generated.
clang -arch arm64 -std=gnu23 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o gaga.so cseqdesma.o cstat.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/gaga.buildbin-libdir/00LOCK-gaga/00new/gaga/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 (gaga)


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

>>>>>>> Paths before fix:
gaga.buildbin-libdir/gaga/libs/gaga.so:
	gaga.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)

>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!