Problems with installation ubuntu 20.04

[spinkney]

I am following http://www.pqr-project.org/INSTALL.txt for Ubuntu. I have created a folder 'pqr-2020-07-23-myconfig' and run the command '~/pqr_source/pqr-2020-07-23-myconfig$ ../pqR-2020-07-23/configure --enable-R-shlib'. After a long list of checks I get the output

R is now configured for x86_64-unknown-linux-gnu, 8-byte pointers

  Source directory:       ../pqR-2020-07-23
  Installation directory: /usr/local

  C compiler:             gcc  -ffp-contract=off -g -O2
  Fortran 77 compiler:    f95  -fno-optimize-sibling-calls -ffp-contract=off -g -O2

  C++ compiler:           g++  -ffp-contract=off -g -O2
  Fortran 90/95 compiler: gfortran  -fno-optimize-sibling-calls -ffp-contract=off -g -O2
  Obj-C compiler:          

  Compressed pointers:    no

  BLAS/LAPACK options:    mat_mult_with_BLAS=FALSE, BLAS_in_helpers=TRUE
                          shared BLAS: built-in, LAPACK: built-in
  External libraries:     readline, ICU, lzma
  Interfaces supported:   X11, tcltk
  Other capabilities:     PNG, JPEG, NLS, ICU
  Other options enabled:  helper threads, task merging, shared R library, R profiling

  Recommended packages:   yes

However when I run the checks I get that bin is not found. Meaning, I cannot open pqR using the /bin/R from the configuration directory since it does not exist.

~/pqr_source/pqr-2020-07-23-myconfig$ make check
make[1]: Entering directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
make[2]: Entering directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
make[3]: Entering directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests/Examples'
/bin/bash: ../../bin/R: No such file or directory
make[3]: *** [Makefile:31: test-Examples-Base] Error 127
make[3]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests/Examples'
make[2]: *** [../../pqR-2020-07-23/tests/Makefile.common:175: test-Examples] Error 2
make[2]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
make[1]: *** [../../pqR-2020-07-23/tests/Makefile.common:165: test-all-basics] Error 1
make[1]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
make: *** [Makefile:217: check] Error 2

[radfordneal]

After running 'configure', did you run 'make' before trying to run 'make check'?

'make check' should maybe automatically run 'make' if bin/R doesn't exists, but it doesn't at the moment.

[spinkney]

When I run make I get an error

make[4]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/src/library/compiler'
make[4]: Entering directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/src/library/compiler'
Error in readRDS(pfile) : 
  cannot read workspace version 3 written by R 4.0.3; need R 3.5.0 or newer
Calls: <Anonymous> ... findpack -> find.package -> lapply -> FUN -> readRDS
Execution halted
make[4]: *** [../../../../pqR-2020-07-23/share/make/basepkg.mk:120: mklazy] Error 1
make[4]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/src/library/compiler'
make[3]: *** [Makefile:27: all] Error 2
make[3]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/src/library/compiler'
make[2]: *** [Makefile:35: R] Error 1
make[2]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/src/library'
make[1]: *** [Makefile:28: R] Error 1
make[1]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/src'
make: *** [Makefile:59: R] Error 1

Knowing that make checks won't work given that make failed, here's the output anyway,

spinkney@ip-1XX:~/pqr_source/pqr-2020-07-23-myconfig$ make check
make[1]: Entering directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
make[2]: Entering directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
make[3]: Entering directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests/Examples'
WARNING: ignoring environment value of R_HOME
During startup - Warning messages:
1: package "methods" in options("defaultPackages") was not found 
2: package ‘datasets’ in options("defaultPackages") was not found 
3: package ‘utils’ in options("defaultPackages") was not found 
4: package ‘grDevices’ in options("defaultPackages") was not found 
5: package ‘graphics’ in options("defaultPackages") was not found 
6: package ‘stats’ in options("defaultPackages") was not found 
7: package ‘methods’ in options("defaultPackages") was not found 
Testing examples for package ‘base’
no parsed files found
Warning: no examples found for package ‘base’
Testing examples for package ‘tools’
no parsed files found
Warning: no examples found for package ‘tools’
Testing examples for package ‘utils’
no parsed files found
Warning: no examples found for package ‘utils’
Testing examples for package ‘grDevices’
no parsed files found
Warning: no examples found for package ‘grDevices’
Testing examples for package ‘graphics’
no parsed files found
Warning: no examples found for package ‘graphics’
Testing examples for package ‘stats’
no parsed files found
Warning: no examples found for package ‘stats’
Testing examples for package ‘datasets’
no parsed files found
Warning: no examples found for package ‘datasets’
Testing examples for package ‘methods’
no parsed files found
Warning: no examples found for package ‘methods’
Testing examples for package ‘grid’
no parsed files found
Warning: no examples found for package ‘grid’
Testing examples for package ‘splines’
no parsed files found
Warning: no examples found for package ‘splines’
Testing examples for package ‘stats4’
no parsed files found
Warning: no examples found for package ‘stats4’
Testing examples for package ‘tcltk’
no parsed files found
Warning: no examples found for package ‘tcltk’
Testing examples for package ‘compiler’
no parsed files found
Warning: no examples found for package ‘compiler’
Testing examples for package ‘parallel’
no parsed files found
Warning: no examples found for package ‘parallel’
make[3]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests/Examples'
make[2]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
make[2]: Entering directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
running strict specific tests
make[3]: Entering directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
running code in '../../pqR-2020-07-23/tests/eval-etc.R' ...make[3]: *** [../../pqR-2020-07-23/tests/Makefile.common:103: eval-etc.Rout] Error 1
make[3]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
make[2]: *** [../../pqR-2020-07-23/tests/Makefile.common:183: test-Specific] Error 2
make[2]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
make[1]: *** [../../pqR-2020-07-23/tests/Makefile.common:165: test-all-basics] Error 1
make[1]: Leaving directory '/home/spinkney/pqr_source/pqr-2020-07-23-myconfig/tests'
make: *** [Makefile:217: check] Error 2

[radfordneal]

It looks like something in your environment is causing pqR to try to read a workspace that you wrote with a recent version of R-core R. You could look at the shell environment with the 'set' command, then unset ones that start with "R" using 'unset'. (This assumes you're using 'bash' as your shell.)

[spinkney]

Thank you, I will have to test once I can unset R since I'm running on a server that other users use.

[radfordneal]

It shouldn't matter that you're on a shared machine, since the environment for your shell is local to you.