install issue

[ChristophKnapp]

Hi, I'm trying to install RcppArmadillo on a debian computer. R version is 4.3.1 (2023-06-16) -- "Beagle Scouts". I'm not sure what the problem is and could not find anything related to

/usr/bin/ld: cannot find -llapack /usr/bin/ld: cannot find -lblas

Most often its just a library missing but with this I'm lost.

I actually try to install the seqinr package where RcppArmadillo is in the dependency tree.

Regards

install.packages("RcppArmadillo") Installing package into ‘/home/hummelchen/R/x86_64-pc-linux-gnu-library/4.3’ (as ‘lib’ is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.12.4.1.0.tar.gz' Content type 'application/x-gzip' length 1373512 bytes (1.3 MB)

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 the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed checking whether we have a suitable tempdir... /tmp checking whether R CMD SHLIB can already compile programs using OpenMP... yes checking LAPACK_LIBS... system LAPACK found configure: creating ./config.status config.status: creating inst/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Debian 10.2.1-6) 10.2.1 20210110’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/hummelchen/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppArmadillo.cpp -o RcppArmadillo.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/hummelchen/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/hummelchen/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fastLm.cpp -o fastLm.o g++ -std=gnu++17 -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:10: RcppArmadillo.so] Error 1 ERROR: compilation failed for package ‘RcppArmadillo’
• removing ‘/home/hummelchen/R/x86_64-pc-linux-gnu-library/4.3/RcppArmadillo’

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

[eddelbuettel]

Please do

  sudo apt install r-base-dev

to get the development packages needed to link against libraries needed, here BLAS and LAPACK. That is a well documented aspect of how life on Linux system works and is similar for the other distros.

Or just do

 sudo apt install r-cran-rcpparmadillo

and enjoy the pre-made package. We provide it so that users unfamiliar with builds do not have to worry about it.

As there is no issue with the source package you reported against, I will close this issue. For general questions on how to use R on Debian, Ubuntu, ... etc the r-sig-debian list is very helpful and would have been a good venue too.

[ChristophKnapp]

That was silly of me, I was so sure I did that. Thanks for your fast help.

[eddelbuettel]

We all had our moments like that. No worries. I hope you get to enjoy RcppArmadillo, by itself or via seqinr.