Which dependency list to build first?

On Wed, 27 Feb 2019, Rainer Krug wrote:

I am sure, you have uninstalled the package completely and tried it

again?

Rainer,

Yes. Just did so with the same result: R could not load the shared library.

Have you tried at looking at the shared objects required by
`/usr/lib/R/library/later/libs/later.so` using ldd ?

Because later was removed and could not be rebuilt, there is no later.so to
be queried for dependencies.

I'll look again at later's dependencies and ensure they're all rebuilt.

Regards,

Rich

Add the --no-test-load option to the install command and the unloadable .so
file should be left there so you can look at its dependencies with, e.g.,
'R CMD ldd .../libs/later.so'.

On Wed, 27 Feb 2019, William Dunlap wrote:

Add the --no-test-load option to the install command and the unloadable

.so

file should be left there so you can look at its dependencies with, e.g.,
'R CMD ldd .../libs/later.so'.

Bill,

Using the syntax 'install.packages("later") --no-test-load' still produces
the same result:

** testing if installed package can be loaded
Error: package or namespace load failed for ?later? in dyn.load(file,
DLLpath = DLLpath, ...):
  unable to load shared object '/usr/lib/R/library/later/libs/later.so':
   /usr/lib/R/library/later/libs/later.so: undefined symbol:
__atomic_fetch_add_8
Error: loading failed
Execution halted
ERROR: loading failed

The later package was installed so why it's not updating now puzzles me.
I'm
running R-3.5.2 on Slackware-14.2.

Regards,

Rich

The syntax is either
   install.packages("later", type="source", INSTALL_opts="--no-test-load")
from within R (perhaps with repos=NULL if from a local directory) or
   R CMD INSTALL --no-test-load later
from outside of R, where 'later' must be a directory.

On Wed, 27 Feb 2019, William Dunlap wrote:

The syntax is either
   install.packages("later", type="source",

INSTALL_opts="--no-test-load")

from within R (perhaps with repos=NULL if from a local directory) or
   R CMD INSTALL --no-test-load later
from outside of R, where 'later' must be a directory.

Bill,

Thank you very much. I read ?install.packages and saw all the options but
had no idea what to use.

Boy howdy! Removing the load testing allowed the package to install:

installing to /usr/lib/R/library/later/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
* DONE (later)

Is it worth exploring why testing loading failed here for this package?

Best regards,

Rich

The package will not load. The only reason to do test load is to examine
why the package's .so file cannot be loaded. We know there is at least one
function or data symbol that it cannot find, __atomic_fetch_add_8, which
may be from boost::atomic. The ldd command may give some hints about
missing libraries.

On Wed, 27 Feb 2019, William Dunlap wrote:

The package will not load. The only reason to do test load is to examine
why the package's .so file cannot be loaded. We know there is at least

one

function or data symbol that it cannot find, __atomic_fetch_add_8, which
may be from boost::atomic. The ldd command may give some hints about
missing libraries.

Bill,

Yes, it does. libR.so is not found:
# ldd later.so
        linux-gate.so.1 (0xb76df000)
        libR.so => not found

However, R runs and libR.so is found here:
/usr/lib/R/lib/libR.so
and was last accessed
-rwxr-xr-x 1 root root 3331940 Dec 23 10:00 /usr/lib/R/lib/libR.so*

Should I rebuild and reinstall R-3.5.2?

Thanks again,

Rich

Did you use 'R CMD ldd .../later.so', as I recommended?

On Wed, 27 Feb 2019, William Dunlap wrote:

Did you use 'R CMD ldd .../later.so', as I recommended?

Bill,

I ran ldd externally on /usr/lib/R/library/lib/later/later.so and posted
the
missing library. Just now I ran the above command and it did not find
later.so:

# R CMD ldd /usr/lib/R/library/later.so
ldd: /usr/lib/R/library/later.so: No such file or directory

Strange. And confusing to me.

Regards,

Rich

These two pathnames are different

/usr/lib/R/library/lib/later/later.so
/usr/lib/R/library/later.so

Was that your intention?