I'm trying to install some of the popular R packages but somehow my R does not see the lapack installation. Or rather the compiler doesn't see it, I guess, because when it checks LAPACK_LIBS it says it found it. I checked sessionInfo() and La_version() and they both point to where lapack is installed. How do I even go about solving it?
> install.packages("RcppArmadillo")
Installing package into ‘/homeUPDATES
/marcin/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.10.5.0.0.tar.gz'
Content type 'application/x-gzip' length 1669395 bytes (1.6 MB)
==================================================
downloaded 1.6 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 g++ -std=gnu++14 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++14 accepts -g... (cached) yes
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/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tbZjLv/r-base-4.1.0=. -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'/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tbZjLv/r-base-4.1.0=. -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'/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tbZjLv/r-base-4.1.0=. -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 -L/usr/local/opt/gsl/lib -lgsl -llapack -lgslcblas -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/usr/local/opt/gettext/lib -L/usr/lib/R/lib -lR
installing to /home/marcin/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs
** R
** 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
Error: package or namespace load failed for ‘RcppArmadillo’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/RcppArmadillo.so':
/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/RcppArmadillo.so: undefined symbol: dgesvx_
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/marcin/R/x86_64-pc-linux-gnu-library/4.1/RcppArmadillo’
Warning in install.packages("RcppArmadillo") :
installation of package ‘RcppArmadillo’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpw0yc9E/downloaded_packages’
>
UPDATE 1:
I made sure that the blas and lapack .so files have 755 permissions but it didn't help.
UPDATE 2:
The same problem occurs when I try to build from source a package that needs lapack. For example, I tried installing the GpGp package with the following Makevars
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
and it gives the same problem.
So eventually I figured out that the problem was my ~/.R/Makevars file. Dirk's comment under my original question made me wonder where do these extra commands come from and I found them in Makevars. I don't remember when and why I added something to it but when I reverted back to just an empty Makevars file everything worked! Thanks Dirk!