[R] Issue building from source on RHEL7

[Stéphane Plaisance]

Dear,

After trying other methods, I finally went for the build from source as detailed on the RStudio site (https://docs.posit.co/resources/install-r-source/).

################
I did the following as per the info on the Posit page:

sudo yum-builddep R

export R_VERSION=4.2.2

curl -O https://cran.rstudio.com/src/base/R-4/R-${R_VERSION}.tar.gz<https://cran.rstudio.com/src/base/R-4/R-$%7bR_VERSION%7d.tar.gz>
$ tar -xzvf R-${R_VERSION}.tar.gz
$ cd R-${R_VERSION}

$ ./configure \
    --prefix=/opt/R \
    --enable-memory-profiling \
    --enable-R-shlib \
    --with-blas \
    --with-lapack

$ make
$ make check
$ sudo make install

I could build R from source and the tests report success


$ make check

make[1]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[2]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[3]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests/Examples'

Testing examples for package ‘base’

Testing examples for package ‘tools’

  comparing ‘tools-Ex.Rout’ to ‘tools-Ex.Rout.save’ ... OK

Testing examples for package ‘utils’

Testing examples for package ‘grDevices’

  comparing ‘grDevices-Ex.Rout’ to ‘grDevices-Ex.Rout.save’ ... OK

Testing examples for package ‘graphics’

  comparing ‘graphics-Ex.Rout’ to ‘graphics-Ex.Rout.save’ ... OK

Testing examples for package ‘stats’

  comparing ‘stats-Ex.Rout’ to ‘stats-Ex.Rout.save’ ... OK

Testing examples for package ‘datasets’

  comparing ‘datasets-Ex.Rout’ to ‘datasets-Ex.Rout.save’ ... OK

Testing examples for package ‘methods’

Testing examples for package ‘grid’

  comparing ‘grid-Ex.Rout’ to ‘grid-Ex.Rout.save’ ... OK

Testing examples for package ‘splines’

  comparing ‘splines-Ex.Rout’ to ‘splines-Ex.Rout.save’ ... OK

Testing examples for package ‘stats4’

  comparing ‘stats4-Ex.Rout’ to ‘stats4-Ex.Rout.save’ ... OK

Testing examples for package ‘tcltk’

Testing examples for package ‘compiler’

Testing examples for package ‘parallel’

make[3]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests/Examples'

make[2]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[2]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

running strict specific tests

make[3]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

running code in 'eval-etc.R' ... OK

  comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK

running code in 'simple-true.R' ... OK

  comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK

running code in 'arith-true.R' ... OK

  comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK

running code in 'arith.R' ... OK

  comparing 'arith.Rout' to './arith.Rout.save' ... OK

running code in 'lm-tests.R' ... OK

  comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK

running code in 'ok-errors.R' ... OK

  comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK

running code in 'method-dispatch.R' ... OK

  comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK

running code in 'any-all.R' ... OK

  comparing 'any-all.Rout' to './any-all.Rout.save' ... OK

running code in 'structure.R' ... OK

  comparing 'structure.Rout' to './structure.Rout.save' ... OK

running code in 'd-p-q-r-tests.R' ... OK

  comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK

make[3]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

running sloppy specific tests

make[3]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

running code in 'complex.R' ... OK

  comparing 'complex.Rout' to './complex.Rout.save' ... OK

running code in 'print-tests.R' ... OK

  comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK

running code in 'lapack.R' ... OK

  comparing 'lapack.Rout' to './lapack.Rout.save' ... OK

running code in 'datasets.R' ... OK

  comparing 'datasets.Rout' to './datasets.Rout.save' ... OK

running code in 'datetime.R' ... OK

  comparing 'datetime.Rout' to './datetime.Rout.save' ... OK

running code in 'iec60559.R' ... OK

  comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK

running code in 'eval-etc-2.R' ... OK

  comparing 'eval-etc-2.Rout' to './eval-etc-2.Rout.save' ... OK

make[3]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[3]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

checking Sys.timezone ...

make[4]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

running code in 'timezone.R' ... OK

make[4]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[3]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[2]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[2]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

running regression tests ...

make[3]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

running code in 'array-subset.R' ... OK

running code in 'reg-tests-1a.R' ... OK

running code in 'reg-tests-1b.R' ... OK

running code in 'reg-tests-1c.R' ... OK

running code in 'reg-tests-1d.R' ... OK

running code in 'reg-tests-2.R' ... OK

  comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK

running code in 'reg-examples1.R' ... OK

running code in 'reg-examples2.R' ... OK

running code in 'reg-packages.R' ... OK

running code in 'p-qbeta-strict-tst.R' ... OK

running code in 'd-p-q-r-tst-2.R' ... OK

running code in 'r-strict-tst.R' ... OK

running code in 'reg-IO.R' ... OK

  comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK

running code in 'reg-IO2.R' ... OK

  comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK

running code in 'reg-plot.R' ... OK

  comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK

running code in 'reg-S4-examples.R' ... OK

running code in 'reg-BLAS.R' ... OK

make[3]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[3]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

running code in 'reg-tests-3.R' ... OK

  comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK

running code in 'reg-examples3.R' ... OK

  comparing 'reg-examples3.Rout' to './reg-examples3.Rout.save' ... OK

running tests of plotting Latin-1

  expect failure or some differences if not in a Latin-1 or UTF-8 locale

running code in 'reg-plot-latin1.R' ... OK

  comparing 'reg-plot-latin1.pdf' to './reg-plot-latin1.pdf.save' ... OK

running code in 'reg-S4.R' ... OK

  comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK

make[3]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[2]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[2]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

running tests of Internet functions

make[3]: Entering directory `/home/splaisan/Downloads/R-4.2.2/tests'

running code in 'internet.R' ... OK

  comparing 'internet.Rout' to './internet.Rout.save' ...39d38

< [24] "</html>"

 OK

make[3]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[2]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

make[1]: Leaving directory `/home/splaisan/Downloads/R-4.2.2/tests'

R almost works when run from the build /bin folder (besides a couple of warnings which I do not understand)


$ bin/R

Error in gzfile(file, "rb") : cannot open the connection

In addition: Warning message:

In gzfile(file, "rb") :

  cannot open compressed file '/usr/lib64/R/library/base/R/base.rdx', probable reason 'No such file or directory'

Error: could not find function "attach"



R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"

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Error: object '.ArgsEnv' not found

Fatal error: unable to initialize the JIT


Then when I run ‘sudo make install’, the prefix path only gets part of the expected folders and the resulting collection is not functional (it lacks even the library folder)

Can you please help me fix this?

Thanks in advance

Stephane


####################################
The resulting opt/R/ folder contains:


$ ll /opt/R/

total 4.0K

drwxr-xr-x.  5 root root   40 Jan  4 17:22 .

drwxr-xr-x. 18 root root 4.0K Jan  4 14:30 ..

drwxr-xr-x.  2 root root   28 Jan  4 17:22 bin

drwxr-xr-x.  4 root root   30 Jan  4 17:22 lib64

drwxr-xr-x.  3 root root   16 Jan  4 17:22 share

which is far from what I have on a functional different server (ubuntu 20)

$ ll /usr/lib/R
total 44K
drwxr-xr-x   8 root root 4.0K Nov 14 09:28 .
drwxr-xr-x 158 root root  12K Nov 18 06:20 ..
drwxr-xr-x   3 root root 4.0K Nov 14 09:28 bin
lrwxrwxrwx   1 root root   33 Nov 12 17:12 COPYING -> ../../share/common-licenses/GPL-2
drwxr-xr-x   2 root root 4.0K Nov 14 09:28 etc
drwxr-xr-x   2 root root 4.0K Nov 14 09:28 lib
drwxr-xr-x  32 root root 4.0K Sep  6 13:07 library
drwxr-xr-x   2 root root 4.0K Nov 14 09:28 modules
drwxr-xr-x   2 root root 4.0K Aug 11 02:31 site-library
-rw-r--r--   1 root root   46 Nov 12 17:12 SVN-REVISION




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