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This page was generated on 2026-04-18 11:37 -0400 (Sat, 18 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 alpha (2026-04-05 r89794) 4957
kjohnson3macOS 13.7.7 Venturaarm644.6.0 alpha (2026-04-08 r89818) 4686
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4627
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2083/2404HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMAD 1.27.5  (landing page)
Qingzhou Zhang
Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026)
git_url: https://git.bioconductor.org/packages/SMAD
git_branch: devel
git_last_commit: de15b0e
git_last_commit_date: 2026-04-17 06:35:28 -0400 (Fri, 17 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    WARNINGS  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  
See other builds for SMAD in R Universe.

BUILD BIN results for SMAD on kjohnson3

To the developers/maintainers of the SMAD package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SMAD.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SMAD
Version: 1.27.5
Command: rm -rf SMAD.buildbin-libdir && mkdir SMAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SMAD_1.27.5.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SMAD.buildbin-libdir
StartedAt: 2026-04-17 23:33:16 -0400 (Fri, 17 Apr 2026)
EndedAt: 2026-04-17 23:33:45 -0400 (Fri, 17 Apr 2026)
EllapsedTime: 29.6 seconds
RetCode: 0
Status:   OK  
PackageFile: SMAD_1.27.5.tgz
PackageFileSize: 1.278 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SMAD.buildbin-libdir && mkdir SMAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SMAD_1.27.5.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SMAD.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SMAD.buildbin-libdir SMAD_1.27.5.tar.gz'
>>>>>>> 

Warning: SystemRequirements specified C++14: support has been removed
* installing *source* package ‘SMAD’ ...
** this is package ‘SMAD’ version ‘1.27.5’
** using staged installation
** libs
specified C++14
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/api/deprecated.c -o nlopt/api/deprecated.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/api/general.c -o nlopt/api/general.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/api/optimize.c -o nlopt/api/optimize.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/api/options.c -o nlopt/api/options.o
nlopt/api/options.c:235:1: warning: non-void function does not return a value [-Wreturn-type]
  235 | }
      | ^
nlopt/api/options.c:257:1: warning: non-void function does not return a value [-Wreturn-type]
  257 | }
      | ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/cobyla/cobyla.c -o nlopt/cobyla/cobyla.o
nlopt/cobyla/cobyla.c:1256:7: warning: variable 'iout' set but not used [-Wunused-but-set-variable]
 1256 |   int iout, i__, j, k;
      |       ^
nlopt/cobyla/cobyla.c:35:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
   35 | static char const rcsid[] =
      |                   ^~~~~
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/auglag/auglag.c -o nlopt/auglag/auglag.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/bobyqa/bobyqa.c -o nlopt/bobyqa/bobyqa.o
nlopt/bobyqa/bobyqa.c:27:20: warning: variable 'jl' set but not used [-Wunused-but-set-variable]
   27 |     int i__, j, k, jl, jp;
      |                    ^
nlopt/bobyqa/bobyqa.c:1182:47: warning: variable 'ratio' set but not used [-Wunused-but-set-variable]
 1182 |     double resid, delsq, ggsav, tempa, tempb, ratio, sqstp, redmax, 
      |                                               ^
nlopt/bobyqa/bobyqa.c:1182:54: warning: variable 'sqstp' set but not used [-Wunused-but-set-variable]
 1182 |     double resid, delsq, ggsav, tempa, tempb, ratio, sqstp, redmax, 
      |                                                      ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/cdirect/cdirect.c -o nlopt/cdirect/cdirect.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/cdirect/hybrid.c -o nlopt/cdirect/hybrid.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/crs/crs.c -o nlopt/crs/crs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/direct/DIRect.c -o nlopt/direct/DIRect.o
nlopt/direct/DIRect.c:71:19: warning: variable 'newtosample' set but not used [-Wunused-but-set-variable]
   71 |     integer pos1, newtosample;
      |                   ^
nlopt/direct/DIRect.c:81:13: warning: variable 'writed' set but not used [-Wunused-but-set-variable]
   81 |     integer writed;
      |             ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/direct/direct_wrap.c -o nlopt/direct/direct_wrap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/direct/DIRserial.c -o nlopt/direct/DIRserial.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/direct/DIRsubrout.c -o nlopt/direct/DIRsubrout.o
nlopt/direct/DIRsubrout.c:505:10: warning: explicitly assigning value of variable of type 'integer' (aka 'int') to itself [-Wself-assign]
  505 |             pos = pos;
      |             ~~~ ^ ~~~
nlopt/direct/DIRsubrout.c:1157:16: warning: variable 'costmin' set but not used [-Wunused-but-set-variable]
 1157 |     doublereal costmin;
      |                ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/isres/isres.c -o nlopt/isres/isres.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/luksan/mssubs.c -o nlopt/luksan/mssubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/luksan/plip.c -o nlopt/luksan/plip.o
nlopt/luksan/plip.c:139:24: warning: variable 'eta0' set but not used [-Wunused-but-set-variable]
  139 |     double alf1, alf2, eta0, eta9, par1, par2;
      |                        ^
nlopt/luksan/plip.c:140:9: warning: variable 'mes1' set but not used [-Wunused-but-set-variable]
  140 |     int mes1, mes2, mes3, met3;
      |         ^
nlopt/luksan/plip.c:140:15: warning: variable 'mes2' set but not used [-Wunused-but-set-variable]
  140 |     int mes1, mes2, mes3, met3;
      |               ^
nlopt/luksan/plip.c:140:21: warning: variable 'mes3' set but not used [-Wunused-but-set-variable]
  140 |     int mes1, mes2, mes3, met3;
      |                     ^
nlopt/luksan/plip.c:142:9: warning: variable 'meta' set but not used [-Wunused-but-set-variable]
  142 |     int meta, mred, nred, iold;
      |         ^
5 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/luksan/plis.c -o nlopt/luksan/plis.o
nlopt/luksan/plis.c:130:24: warning: variable 'eta0' set but not used [-Wunused-but-set-variable]
  130 |     double alf1, alf2, eta0, eta9, par1, par2;
      |                        ^
nlopt/luksan/plis.c:131:9: warning: variable 'mes1' set but not used [-Wunused-but-set-variable]
  131 |     int mes1, mes2, mes3;
      |         ^
nlopt/luksan/plis.c:131:15: warning: variable 'mes2' set but not used [-Wunused-but-set-variable]
  131 |     int mes1, mes2, mes3;
      |               ^
nlopt/luksan/plis.c:131:21: warning: variable 'mes3' set but not used [-Wunused-but-set-variable]
  131 |     int mes1, mes2, mes3;
      |                     ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/luksan/pnet.c -o nlopt/luksan/pnet.o
nlopt/luksan/pnet.c:159:9: warning: variable 'mes1' set but not used [-Wunused-but-set-variable]
  159 |     int mes1, mes2, mes3;
      |         ^
nlopt/luksan/pnet.c:159:15: warning: variable 'mes2' set but not used [-Wunused-but-set-variable]
  159 |     int mes1, mes2, mes3;
      |               ^
nlopt/luksan/pnet.c:159:21: warning: variable 'mes3' set but not used [-Wunused-but-set-variable]
  159 |     int mes1, mes2, mes3;
      |                     ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/luksan/pssubs.c -o nlopt/luksan/pssubs.o
nlopt/luksan/pssubs.c:527:18: warning: variable 'c__' set but not used [-Wunused-but-set-variable]
  527 |     double a, b, c__, aa, bb, ah, den, par, pom;
      |                  ^
nlopt/luksan/pssubs.c:656:18: warning: variable 'c__' set but not used [-Wunused-but-set-variable]
  656 |     double a, b, c__, aa, bb, cc, ah, den, par, pom, zet;
      |                  ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/mlsl/mlsl.c -o nlopt/mlsl/mlsl.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/mma/ccsa_quadratic.c -o nlopt/mma/ccsa_quadratic.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/mma/mma.c -o nlopt/mma/mma.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/neldermead/nldrmd.c -o nlopt/neldermead/nldrmd.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/neldermead/sbplx.c -o nlopt/neldermead/sbplx.o
nlopt/neldermead/sbplx.c:78:13: warning: variable 'fprev' set but not used [-Wunused-but-set-variable]
   78 |      double fprev;
      |             ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/newuoa/newuoa.c -o nlopt/newuoa/newuoa.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/praxis/praxis.c -o nlopt/praxis/praxis.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/slsqp/slsqp.c -o nlopt/slsqp/slsqp.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/util/mt19937ar.c -o nlopt/util/mt19937ar.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/util/qsort_r.c -o nlopt/util/qsort_r.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/util/redblack.c -o nlopt/util/redblack.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/util/rescale.c -o nlopt/util/rescale.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/util/sobolseq.c -o nlopt/util/sobolseq.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/util/stop.c -o nlopt/util/stop.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Inlopt/auglag -Inlopt/bobyqa -Inlopt/cdirect -Inlopt/crs -Inlopt/direct -Inlopt/isres -Inlopt/luksan -Inlopt/mlsl -Inlopt/mma -Inlopt/neldermead -Inlopt/newuoa -Inlopt/praxis -Inlopt/slsqp -DHAVE_COPYSIGN -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_STDINT_H -DHAVE_UNISTD_H -DHAVE_TIME -DHAVE_GETTIMEOFDAY -fPIC  -falign-functions=64 -Wall -g -O2  -c nlopt/util/timer.c -o nlopt/util/timer.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c saint_common/BaitClass.cpp -o saint_common/BaitClass.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c saint_common/PreyClass.cpp -o saint_common/PreyClass.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c saint_common/InterClass.cpp -o saint_common/InterClass.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c saint_common/UIClass.cpp -o saint_common/UIClass.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c saint_spc/SpcStats.cpp -o saint_spc/SpcStats.o
saint_spc/SpcStats.cpp:62:3: warning: unused label 'mu_init' [-Wunused-label]
   62 |                 mu_init: 
      |                 ^~~~~~~~
saint_spc/SpcStats.cpp:261:23: warning: braces around scalar initializer [-Wbraced-scalar-init]
  261 |         opt.set_lower_bounds({-15});
      |                              ^~~~~
saint_spc/SpcStats.cpp:262:23: warning: braces around scalar initializer [-Wbraced-scalar-init]
  262 |         opt.set_upper_bounds({ 15});
      |                              ^~~~~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c saint_spc/SpcStats_fns.cpp -o saint_spc/SpcStats_fns.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c saint_spc/SpcMapping.cpp -o saint_spc/SpcMapping.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c SpcEntry.cpp -o SpcEntry.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c saint_int/IntStats.cpp -o saint_int/IntStats.o
saint_int/IntStats.cpp:92:6: warning: unused variable 'L' [-Wunused-variable]
   92 |         int L = min<size_t>(n_ctrl_ip, L_user_input);
      |             ^
saint_int/IntStats.cpp:204:9: warning: variable 'tmpsum' set but not used [-Wunused-but-set-variable]
  204 |         double tmpsum=0,countsum=0;
      |                ^
saint_int/IntStats.cpp:204:18: warning: variable 'countsum' set but not used [-Wunused-but-set-variable]
  204 |         double tmpsum=0,countsum=0;
      |                         ^
saint_int/IntStats.cpp:324:23: warning: braces around scalar initializer [-Wbraced-scalar-init]
  324 |         opt.set_lower_bounds({-15});
      |                              ^~~~~
saint_int/IntStats.cpp:325:23: warning: braces around scalar initializer [-Wbraced-scalar-init]
  325 |         opt.set_upper_bounds({ 15});
      |                              ^~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c saint_int/IntMapping.cpp -o saint_int/IntMapping.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c IntEntry.cpp -o IntEntry.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c GetDICE.cpp -o GetDICE.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c GetPPN.cpp -o GetPPN.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include   -Inlopt/api -Inlopt -Inlopt/cobyla -Inlopt/util -Isaint_common -Isaint_spc -Isaint_int -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.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 SMAD.so nlopt/api/deprecated.o nlopt/api/general.o nlopt/api/optimize.o nlopt/api/options.o nlopt/cobyla/cobyla.o nlopt/auglag/auglag.o nlopt/bobyqa/bobyqa.o nlopt/cdirect/cdirect.o nlopt/cdirect/hybrid.o nlopt/crs/crs.o nlopt/direct/DIRect.o nlopt/direct/direct_wrap.o nlopt/direct/DIRserial.o nlopt/direct/DIRsubrout.o nlopt/isres/isres.o nlopt/luksan/mssubs.o nlopt/luksan/plip.o nlopt/luksan/plis.o nlopt/luksan/pnet.o nlopt/luksan/pssubs.o nlopt/mlsl/mlsl.o nlopt/mma/ccsa_quadratic.o nlopt/mma/mma.o nlopt/neldermead/nldrmd.o nlopt/neldermead/sbplx.o nlopt/newuoa/newuoa.o nlopt/praxis/praxis.o nlopt/slsqp/slsqp.o nlopt/util/mt19937ar.o nlopt/util/qsort_r.o nlopt/util/redblack.o nlopt/util/rescale.o nlopt/util/sobolseq.o nlopt/util/stop.o nlopt/util/timer.o saint_common/BaitClass.o saint_common/PreyClass.o saint_common/InterClass.o saint_common/UIClass.o saint_spc/SpcStats.o saint_spc/SpcStats_fns.o saint_spc/SpcMapping.o SpcEntry.o saint_int/IntStats.o saint_int/IntMapping.o IntEntry.o GetDICE.o GetPPN.o RcppExports.o -lm -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/SMAD.buildbin-libdir/00LOCK-SMAD/00new/SMAD/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 (SMAD)


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

>>>>>>> Paths before fix:
SMAD.buildbin-libdir/SMAD/libs/SMAD.so:
	SMAD.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
	/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libgcc_s.1.1.dylib" "SMAD.buildbin-libdir/SMAD/libs/SMAD.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libgfortran.5.dylib" "SMAD.buildbin-libdir/SMAD/libs/SMAD.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libquadmath.0.dylib" "SMAD.buildbin-libdir/SMAD/libs/SMAD.so"

>>>>>>> Paths after fix:
SMAD.buildbin-libdir/SMAD/libs/SMAD.so:
	SMAD.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
	/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)