installation issue: ld: library not found for -lquadmath #262

angieshen6 · 2019-07-16T01:47:24Z

After downloading R.3.6.1, I can no longer install RcppArmadillo. I have Mac OS X El Capitan 10.11.5. I downloaded gfortran 6.1, clang-7 and Xcode following the instructions on here [(https://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-macos/)] but received the following messages:

`=================================================
downloaded 1.3 MB

installing source package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ -std=gnu++11 accepts -g... (cached) yes
checking whether g++ version is sufficient... almost
configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++.
checking for macOS... found
checking for macOS Apple compiler... not found
checking for clang compiler... found
checking for OpenMP compatible version of clang... found and suitable
checking LAPACK_LIBS... R-supplied partial LAPACK found
configure: WARNING: Some complex-valued LAPACK functions may not be available
checking for OpenMP... found and suitable
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fopenmp -fPIC -Wall -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fopenmp -fPIC -Wall -g -O2 -c fastLm.cpp -o fastLm.o
clang++ -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 RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lquadmath
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo’
Warning in install.packages :
installation of package ‘RcppArmadillo’ had non-zero exit status`

coatless · 2019-07-16T02:01:42Z

Type in R:

Sys.getenv("PATH")

Place the results in this issue.

I don't think that the gfortran binary was correctly installed.

angieshen6 · 2019-07-16T02:07:48Z

Sys.getenv("PATH")
[1] "/usr/local/clang7/bin:/usr/local/clang7/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Library/TeX/texbin"

coatless · 2019-07-16T02:16:10Z

Can you try installing the gfortran 6.1 binary again?

https://cran.r-project.org/bin/macosx/tools/gfortran-6.1.pkg

angieshen6 · 2019-07-16T02:23:01Z

Received these messages after reinstallation:

checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ -std=gnu++11 accepts -g... (cached) yes
checking whether g++ version is sufficient... almost
configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++.
checking for macOS... found
checking for macOS Apple compiler... not found
checking for clang compiler... found
checking for OpenMP compatible version of clang... found and suitable
checking LAPACK_LIBS... R-supplied partial LAPACK found
configure: WARNING: Some complex-valued LAPACK functions may not be available
checking for OpenMP... found and suitable
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fopenmp -fPIC  -Wall -g -O2  -c RcppArmadillo.cpp -o RcppArmadillo.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fopenmp -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I../inst/include -fopenmp -fPIC  -Wall -g -O2  -c fastLm.cpp -o fastLm.o
clang++ -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 RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so, 6): Symbol not found: ___cxa_uncaught_exceptions
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib
  Expected in: /usr/lib/libc++abi.dylib
 in /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘RcppArmadillo’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo’
Warning in install.packages :
  installation of package ‘RcppArmadillo’ had non-zero exit status

eddelbuettel · 2019-07-16T09:50:41Z

So that addressed the 'missing Fortran library' but now it looks like a possible mismatch. Does the rest of your clang toolchain come from the same directory, ie https://cran.r-project.org/bin/macosx/tools/ ?

eddelbuettel · 2019-07-16T09:52:48Z

FWIW CRAN still builds them fine https://cloud.r-project.org/web/checks/check_results_RcppArmadillo.html but has not yet gotten to the very fresh (uploaded yesterday) 0.9.600.4.0 release.

dselivanov · 2019-07-16T11:16:02Z

I think I run into similar issue yesterday when I was digging about rcnst issues in my rsparse pkg. I pulled rocker/drd and installed RcppArmadillo 0.9.600.4.0.

I got following error:

* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++11 accepts -g... (cached) yes
checking whether g++ version is sufficient... yes, with OpenMP as version 8.3.0
checking for macOS... checking LAPACK_LIBS... system LAPACK found
checking for OpenMP... found and suitable
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"  -I../inst/include -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"  -I../inst/include -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"  -I../inst/include -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastLm.cpp -o fastLm.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/usr/local/lib/R/site-library/RcppArmadillo’

The downloaded source packages are in
	‘/tmp/RtmpxJFa0T/downloaded_packages’
Warning message:
In install.packages("RcppArmadillo") :
  installation of package ‘RcppArmadillo’ had non-zero exit status

I didn't have time to debug, so I installed libopenblas-dev and issue gone. But I think problem remains (and just reproduced it locally)

eddelbuettel · 2019-07-16T11:57:05Z

@dselivanov I am not sure how relevant that is. You are on a different operating system where we always needed BLAS because we have

edd@rob:~$ grep PKG_LIBS git/rcpparmadillo/src/Makevars.in 
PKG_LIBS= @OPENMP_FLAG@ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
edd@rob:~$

But what does have to do with the OP's problem on macOS?

dselivanov · 2019-07-16T12:35:03Z

My understanding was that RcppArmadillo should link to either R provided reference blas, lapack or system ones. So in case of missing system blas and lapack it should link to the one provided by R (and which in fact was discovered during configure run). So I thought there was something broken with linker starting from R 3.6.1. However I've just checked r-base:3.6.1 image and opposed to rocker/drd it works fine...

…

On Tue, Jul 16, 2019 at 3:57 PM Dirk Eddelbuettel ***@***.***> wrote: @dselivanov <https://github.com/dselivanov> I am not sure how relevant that is. You are on a different operating system *where we always needed BLAS* because we have ***@***.***:~$ grep PKG_LIBS git/rcpparmadillo/src/Makevars.in PKG_LIBS= @OPENMP_FLAG@ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) ***@***.***:~$ But what does have to do with the OP's problem on macOS? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#262?email_source=notifications&email_token=ABHC5XJUB6KFOYJPSYXQR3DP7WZRHA5CNFSM4ID4HSR2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2ATRPY#issuecomment-511785151>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABHC5XIFGNSUSEPXNYEE2QLP7WZRHANCNFSM4ID4HSRQ> .

-- Regards Dmitriy Selivanov

angieshen6 · 2019-07-16T13:21:22Z

@eddelbuettel I reinstalled clang-7 from that site and received the same error messages.

eddelbuettel · 2019-07-16T13:36:54Z

@angieshen6 Beats me. I don't use or support macOS besides what CRAN requires. Plead with @coatless to help you or try the r-sig-mac mailing list.

eddelbuettel · 2019-07-16T13:39:56Z

@dselivanov I still don't understand what that has to do with this issue ticket. Maybe you documented that rocker/drd is not RcppArmadillo ready because it is narrower but there is no bug in the RcppArmadillo package I can discern in your messages. It's early, and I only had four coffees so far so I may be missing something obvious though....

dselivanov · 2019-07-16T13:42:33Z

You are right, nothing to do with rcpparmadillo. False alarm

eddelbuettel · 2019-07-16T13:47:33Z

No worries. Life is about trading off true and false positives :)

coatless · 2019-07-18T14:46:04Z

@angieshen6

You might need to do a full reinstall once the correct toolchain is in use.

Try:

install.packages("RcppArmadillo", 
                 dependencies=TRUE,
                 repos="https://cloud.r-project.org")

Fredo-XVII · 2019-08-30T16:18:28Z

I was getting an error when installing the 'fable' package. But @coatless install code above did the trick to get 'RcppAmrmadillo' installed. Thanks!

eddelbuettel · 2019-08-30T16:22:22Z

Closing this. Please tell the macOS maintainer for R to streamline his process. The package can only work when components are in places, and besides the package-level Depends:/Imports:/... we have no control over where and when. Hence also no ability to affect it.

barracuda156 · 2021-11-26T02:44:15Z

I am getting the same error:

ld: warning: directory not found for option '-L/opt/local/Library/Frameworks/R.framework/Resources/libppc'
ld: library not found for -lquadmath

Is there a solution?

eddelbuettel · 2021-11-26T05:17:33Z

@barracuda156 This is, I think, the third repo I see you use for your questions about your (if I dare say, somewhat non-standard) setup. Can you maybe get some help from people using the os and hardware combination, maybe via the r-sig-mac list? We don't use it -- and the software we provide works everywhere else (where we can test it too) so we cannot help you.

eddelbuettel closed this as completed Aug 30, 2019

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installation issue: ld: library not found for -lquadmath #262

installation issue: ld: library not found for -lquadmath #262

angieshen6 commented Jul 16, 2019

coatless commented Jul 16, 2019 •

edited

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barracuda156 commented Nov 26, 2021

eddelbuettel commented Nov 26, 2021

installation issue: ld: library not found for -lquadmath #262

installation issue: ld: library not found for -lquadmath #262

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angieshen6 commented Jul 16, 2019

coatless commented Jul 16, 2019 • edited Loading

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coatless commented Jul 16, 2019 •

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