Hi, I can not install packages from source which links to RcppArmadillo on Ubuntu 20.04 (after upgrading from 18.04). The following problem occurs:
** testing if installed package can be loaded from temporary location Error: package or namespace load failed for 'myPackage' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib/R/site-library/00LOCK-my_package/00new/myPackage/libs/myPackage.so': /usr/local/lib/R/site-library/00LOCK-my_package/00new/myPackge/libs/myPackage.so: undefined symbol: dgesvx_ Error: loading failed Execution halted ERROR: loading failed This dgesvx_ looked to me like a LAPACK problem ( https://www.netlib.org/lapack/explore-html/d7/d3b/group__double_g_esolve_ga9d90ccf6e340cacd08b7bbbb502ceb21.html#ga9d90ccf6e340cacd08b7bbbb502ceb21 ). I was playing with different BLAS/LAPACK versions on my system and researching this for a couple of days now but without success. I was first looking at which LAPACK and BLAS R is "using" user@user:~$ ps aux | grep exec/R user+ 11663 1.9 1.7 1030952 415240 pts/0 Sl+ 06:33 0:13 /usr/lib/R/bin/exec/R --vanilla --quiet user+ 13836 2.5 0.2 441664 52024 pts/1 Sl+ 06:44 0:00 /usr/lib/R/bin/exec/R user+ 13932 0.0 0.0 8900 660 pts/2 S+ 06:45 0:00 grep exec/R user@user:~$ lsof -p 13836 | grep 'blas\|lapack' R 13836 user mem REG 8,1 33562376 3961750 /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 R 13836 user mem REG 8,1 27200552 3961749 /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 user@user:~$ ls -l /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 -rw-r--r-- 1 root root 27200552 Jun 2 06:55 /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 user@user:~$ ls -l /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 -rw-r--r-- 1 root root 33562376 Jun 2 06:55 /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 And then tried different versions: user@user:~$ sudo update-alternatives --config libblas.so.3-x86_64-linux-gnu There are 4 choices for the alternative libblas.so.3-x86_64-linux-gnu (providing /usr/lib/x86_64-linux-gnu/libblas.so.3). Selection Path Priority Status ------------------------------------------------------------ * 0 /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 100 auto mode 1 /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3 35 manual mode 2 /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 manual mode 3 /usr/lib/x86_64-linux-gnu/openblas-openmp/libblas.so.3 95 manual mode 4 /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 100 manual mode Press <enter> to keep the current choice[*], or type selection number: 3 update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-openmp/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in manual mode user@user:~$ sudo update-alternatives --config liblapack.so.3-x86_64-linux-gnu There are 4 choices for the alternative liblapack.so.3-x86_64-linux-gnu (providing /usr/lib/x86_64-linux-gnu/liblapack.so.3). Selection Path Priority Status ------------------------------------------------------------ * 0 /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 100 auto mode 1 /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3 35 manual mode 2 /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 manual mode 3 /usr/lib/x86_64-linux-gnu/openblas-openmp/liblapack.so.3 95 manual mode 4 /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 100 manual mode Press <enter> to keep the current choice[*], or type selection number: 3 update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-openmp/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in manual mode user@user:~$ sudo update-alternatives --config libblas.so.3-x86_64-linux-gnu There are 4 choices for the alternative libblas.so.3-x86_64-linux-gnu (providing /usr/lib/x86_64-linux-gnu/libblas.so.3). Selection Path Priority Status ------------------------------------------------------------ 0 /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 100 auto mode 1 /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3 35 manual mode 2 /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 manual mode * 3 /usr/lib/x86_64-linux-gnu/openblas-openmp/libblas.so.3 95 manual mode 4 /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 100 manual mode Press <enter> to keep the current choice[*], or type selection number: 2 update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in manual mode user@user:~$ sudo update-alternatives --config liblapack.so.3-x86_64-linux-gnu There are 4 choices for the alternative liblapack.so.3-x86_64-linux-gnu (providing /usr/lib/x86_64-linux-gnu/liblapack.so.3). Selection Path Priority Status ------------------------------------------------------------ 0 /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 100 auto mode 1 /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3 35 manual mode 2 /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 manual mode * 3 /usr/lib/x86_64-linux-gnu/openblas-openmp/liblapack.so.3 95 manual mode 4 /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 100 manual mode Press <enter> to keep the current choice[*], or type selection number: 2 update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in manual mode I have no idea what could be wrong here... Thanks in advance for hints and help on what to do here. Best regards, Sam [[alternative HTML version deleted]] _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian