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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL casper
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘casper’ ...
** this is package ‘casper’ version ‘2.45.2’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c casper.cpp -o casper.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cstat.cpp -o cstat.o
cstat.cpp:17:19: warning: unused variable 'interface_c_sccs_id' [-Wunused-const-variable]
   17 | static const char interface_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~~~~~~
cstat.cpp:18:19: warning: unused variable 'mess_c_sccs_id' [-Wunused-const-variable]
   18 | static const char mess_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~
cstat.cpp:19:19: warning: unused variable 'nrutil_c_sccs_id' [-Wunused-const-variable]
   19 | static const char nrutil_c_sccs_id[] = "%W%"; 
      |                   ^~~~~~~~~~~~~~~~
cstat.cpp:20:19: warning: unused variable 'vector_c_sccs_id' [-Wunused-const-variable]
   20 | static const char vector_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~~~
cstat.cpp:21:19: warning: unused variable 'rand_c_sccs_id' [-Wunused-const-variable]
   21 | static const char rand_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
      |                   ^~~~~~~~~~~~~~
cstat.cpp:22:19: warning: unused variable 'cstat_c_sccs_id' [-Wunused-const-variable]
   22 | static const char cstat_c_sccs_id[] = "@(#)$Workfile: cstat.c$ $Revision: 2011-08-23$";
      |                   ^~~~~~~~~~~~~~~
6 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c dataframe.cpp -o dataframe.o
dataframe.cpp:503:31: warning: unused variable 'itexon' [-Wunused-variable]
  503 |       vector<Exon*>::iterator itexon;
      |                               ^~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c discretedf.cpp -o discretedf.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c dropVariant.cpp -o dropVariant.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c exon.cpp -o exon.o
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 fragFunc.c -o fragFunc.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fragment.cpp -o fragment.o
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 functions.c -o functions.o
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 hash.c -o hash.o
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 join_exons.c -o join_exons.o
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 makeIslands.c -o makeIslands.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c model.cpp -o model.o
model.cpp:147:3: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
  147 |                 sprintf(str, "%s {%s}", str, vstr);
      |                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
  278 | __deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
      | ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
  227 |         #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
      |                                                       ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c model_cmp.cpp -o model_cmp.o
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 pathCounts.c -o pathCounts.o
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 procBam.c -o procBam.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcasper.cpp -o rcasper.o
rcasper.cpp:1083:17: warning: variable 'nrowexons' set but not used [-Wunused-but-set-variable]
 1083 |           int rowid=0, nrowexons=0;
      |                        ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c seppel.cpp -o seppel.o
seppel.cpp:484:2: warning: 'delete[]' applied to a pointer that was allocated with 'new'; did you mean 'delete'? [-Wmismatched-new-delete]
  484 |         delete [] possiblemodels;
      |         ^      ~~
seppel.cpp:402:36: note: allocated with 'new' here
  402 |   vector<Model*>* possiblemodels = new vector<Model*>();
      |                                    ^
seppel.cpp:440:6: warning: variable 'accepted' set but not used [-Wunused-but-set-variable]
  440 |         int accepted = 0;
      |             ^
seppel.cpp:506:6: warning: variable 'accepted' set but not used [-Wunused-but-set-variable]
  506 |         int accepted = 0;
      |             ^
3 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 simReads.c -o simReads.o
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 simReadsfunc.c -o simReadsfunc.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c smartmodeldist.cpp -o smartmodeldist.o
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 uniqQname.c -o uniqQname.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c variant.cpp -o variant.o
variant.cpp:164:38: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
  164 |         for (int e = 0; e < exonCount; e++) sprintf(str, "%s,%i", str, exons[e]->id);
      |                                             ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/_stdio.h:278:1: note: 'sprintf' has been explicitly marked deprecated here
  278 | __deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
      | ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/sys/cdefs.h:227:48: note: expanded from macro '__deprecated_msg'
  227 |         #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
      |                                                       ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c variant_cmp.cpp -o variant_cmp.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o casper.so casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-casper/00new/casper/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘transcripts’ in package ‘casper’
** 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 (casper)