I have successfully installed Mosek on my Mac OS X machine (and executed it from the command line), but unfortunately I have fatal errors when I try to install RMosek.
Platform: Mac OS, 64 bit Intel , Catalina 10.15.7. x86_64-apple-darwin17.0
I have installed Xcode and the Command Line Software for Xcode.
My mosek package is in /usr/local/ and I have an academic license in the folder. I run
attachbuilder(what_mosek_bindir="/usr/local/mosek/9.3/tools/platform/osx64x86/bin", pos=2L, name="Rmosek:builder", warn.conflicts=TRUE)
I copy the log from running below, but the gist is that the installation fails when testing if the installed package can be loaded from temporary location. I'm a bit at a loss at to what could be causing this and the error is not sufficiently helpful to give me any ideas. Does anyone have a suggestion?
source("/usr/local/mosek/9.3/tools/platform/osx64x86/rmosek/builder.R")
You may now call 'attachbuilder()' with optional extra arguments:
attachbuilder(what_mosek_bindir="/usr/local/mosek/9.3/tools/platform/osx64x86/bin", pos=2L, name="Rmosek:builder", warn.conflicts=TRUE)
to attach builder functions (e.g., 'install.rmosek') to the search path.
> attachbuilder(what_mosek_bindir="/usr/local/mosek/9.3/tools/platform/osx64x86/bin", pos=2L, name="Rmosek:builder", warn.conflicts=TRUE)
NOTE: Overwriting the database 'Rmosek:builder' on the search path.
Functions attached to the search path:
install.rmosek - install Rmosek package.
update.rmosek - update Rmosek package.
remove.rmosek - remove Rmosek package.
The *.rmosek functions wrap the corresponding utils::*.packages functions
with the following default argument values:
pkgs = "Rmosek"
repos = "
https://download.mosek.com/R/9.3"
configuration variables:
MSK_BINDIR = "/usr/local/mosek/9.3/tools/platform/osx64x86/bin"
# if empty, autoconfigured from mosek executable on PATH.
MSK_HEADERDIR = "/usr/local/mosek/9.3/tools/platform/osx64x86/h"
# if empty, autoconfigured from 'MSK_BINDIR'.
MSK_LIB = "mosek64"
# if empty, autoconfigured from 'MSK_BINDIR'.
and installation styles:
using_pkgbuild = FALSE
# whether to execute in the 'pkgbuild' environment
# as is recommended on Windows to resolve Rtools.
using_sysenv = FALSE
# whether to transmit configuration variables via Sys.setenv()
# as opposed to configure.vars.
See, e.g., `show(install.rmosek)` for its implementation.
install.rmosek()
trying URL '
https://download.mosek.com/R/9.3/src/contrib/Rmosek_9.3.2.tar.gz'
Content type 'application/x-tar' length 1555385 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
* installing *source* package ‘Rmosek’ ...
** using staged installation
Configuring for a UNIX-alike platform (sub-architecture: "")
Found package 'Matrix' version 1.4.0
Found configuration variables in environment
Using MOSEK bin directory: /usr/local/mosek/9.3/tools/platform/osx64x86/bin
Using MOSEK header directory: /usr/local/mosek/9.3/tools/platform/osx64x86/h
Using MOSEK library: mosek64
Configuration done.
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Rmosek.cc -o Rmosek.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c local_stubs.cc -o local_stubs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_globalvars.cc -o rmsk_globalvars.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_msg_base.cc -o rmsk_msg_base.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_msg_mosek.cc -o rmsk_msg_mosek.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_obj_arguments.cc -o rmsk_obj_arguments.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_obj_constraints.cc -o rmsk_obj_constraints.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_obj_matrices.cc -o rmsk_obj_matrices.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_obj_mosek.cc -o rmsk_obj_mosek.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_obj_qobj.cc -o rmsk_obj_qobj.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_obj_sexp.cc -o rmsk_obj_sexp.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_utils_interface.cc -o rmsk_utils_interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_utils_mosek.cc -o rmsk_utils_mosek.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/mosek/9.3/tools/platform/osx64x86/h -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Matrix/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmsk_utils_sexp.cc -o rmsk_utils_sexp.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rmosek.so Rmosek.o local_stubs.o rmsk_globalvars.o rmsk_msg_base.o rmsk_msg_mosek.o rmsk_obj_arguments.o rmsk_obj_constraints.o rmsk_obj_matrices.o rmsk_obj_mosek.o rmsk_obj_qobj.o rmsk_obj_sexp.o rmsk_utils_interface.o rmsk_utils_mosek.o rmsk_utils_sexp.o -L/usr/local/mosek/9.3/tools/platform/osx64x86/bin -lmosek64 -Wl,-rpath,/usr/local/mosek/9.3/tools/platform/osx64x86/bin -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/usr/bin/install_name_tool -change libmosek64.9.3.dylib /usr/local/mosek/9.3/tools/platform/osx64x86/bin/libmosek64.9.3.dylib Rmosek.so
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rmosek/00new/Rmosek/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
sh: line 1: 66181 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/j9/cmyn2ly12n12gdj60y18x1nr0000gn/T//Rtmp1LZEHL/file1022c6e55f3ec'
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rmosek’
Warning in install.packages :
installation of package ‘Rmosek’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/j9/cmyn2ly12n12gdj60y18x1nr0000gn/T/Rtmp5OfW3k/downloaded_packages’