Which dependency list to build first?

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Which dependency list to build first?

Rich Shepard
I apologize for the ambiguous subject; I could not think of a more accurate
one.

Updating packages reported that 'later' did not build, but I did not see
which dependency needs updating. Looking at the CRAN page for this package I
see potentials and would like advice on which are the ones needing explicit
updating:

LinkingTo: Rcpp, BH
Suggests: knitr, rmarkdown, testthat
...
Reverse imports: eplusr, fiery, httpuv, pool, promises, shiny
Reverse linking to: httpuv, promises
Reverse suggests: blogdown, servr

Learning which package(s) need to be rebuilt here for 'later' will help me
the next time I encounter this situaion.

TIA,

Rich

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Re: Which dependency list to build first?

Martin Maechler
>>>>> Rich Shepard
>>>>>     on Sun, 24 Feb 2019 11:08:43 -0800 writes:

    > I apologize for the ambiguous subject; I could not think of a more accurate
    > one.

    > Updating packages reported that 'later' did not build, but I did not see
    > which dependency needs updating. Looking at the CRAN page for this package I
    > see potentials and would like advice on which are the ones needing explicit
    > updating:

    > LinkingTo: Rcpp, BH
    > Suggests: knitr, rmarkdown, testthat
    > ...
    > Reverse imports: eplusr, fiery, httpuv, pool, promises, shiny
    > Reverse linking to: httpuv, promises
    > Reverse suggests: blogdown, servr

I'm not the expert on these problems, but as nobody else has
replied:

My experience is that both Rcpp and BH need  "often" to be
re-installed if your system updates in some way.
IIUC, 'LinkingTo:'  is actually a misnomer (as e.g. the Rcpp maintainer
          has known and told us about often enough),
here, because it's more a "including C++ header templates from"

So, I'd re-install first  Rcpp, then BH,  and then "your"
package.

Please let us (= the audience) know if that helped.

Best,
Martin

    > Learning which package(s) need to be rebuilt here for 'later' will help me
    > the next time I encounter this situaion.

    > TIA,

    > Rich

    > ______________________________________________
    > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
    > https://stat.ethz.ch/mailman/listinfo/r-help
    > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    > and provide commented, minimal, self-contained, reproducible code.

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Re: Which dependency list to build first?

Rich Shepard
On Tue, 26 Feb 2019, Martin Maechler wrote:

> I'm not the expert on these problems, but as nobody else has
> replied:

Martin,

Thanks for responding.

> My experience is that both Rcpp and BH need  "often" to be re-installed if
> your system updates in some way. IIUC, 'LinkingTo:' is actually a misnomer
> (as e.g. the Rcpp maintainer has known and told us about often enough),
> here, because it's more a "including C++ header templates from"
>
> So, I'd re-install first  Rcpp, then BH,  and then "your"
> package.

Did this, and ...

> Please let us (= the audience) know if that helped.

there's still an unresolved issue with package 'later':

** 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
* removing ‘/usr/lib/R/library/later’
* restoring previous ‘/usr/lib/R/library/later’

I urge everyone with more ideas to share them.

Regards,

Rich

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Re: Which dependency list to build first?

Rich Shepard
On Wed, 27 Feb 2019, Rainer Krug wrote:

> I am sure, you have uninstalled the package completely and tried it again?
>
> Have you tried at looking at the shared objects required by `
> /usr/lib/R/library/later/libs/later.so` using ldd ?
>
> I had similar problems on Mac (with other packages) and re-installing some
> home-brew packages fixed it.

Rainer,

In truth, I've ignored the issue for now. :-) Regardless, I will take your
advice and report results when completed.

Thanks very much,

Rich

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Re: Which dependency list to build first?

Rich Shepard
In reply to this post by Rich Shepard
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

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Re: Which dependency list to build first?

R help mailing list-2
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 Dunlap
TIBCO Software
wdunlap tibco.com


On Wed, Feb 27, 2019 at 9:40 AM Rich Shepard <[hidden email]>
wrote:

> 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
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

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Re: Which dependency list to build first?

Rich Shepard
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

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Re: Which dependency list to build first?

R help mailing list-2
    Using the syntax 'install.packages("later") --no-test-load'

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 Dunlap
TIBCO Software
wdunlap tibco.com


On Wed, Feb 27, 2019 at 11:14 AM Rich Shepard <[hidden email]>
wrote:

> 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
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

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Re: Which dependency list to build first?

Rich Shepard
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

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Re: Which dependency list to build first?

R help mailing list-2
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, wihch
may be from boost::atomic.  The ldd command may give some hints about
missing libraries.
Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Wed, Feb 27, 2019 at 11:56 AM Rich Shepard <[hidden email]>
wrote:

> 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
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

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Re: Which dependency list to build first?

Rich Shepard
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

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Re: Which dependency list to build first?

R help mailing list-2
Did you use 'R CMD ldd .../later.so', as I recommended?

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Wed, Feb 27, 2019 at 12:51 PM Rich Shepard <[hidden email]>
wrote:

> 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
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

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Re: Which dependency list to build first?

Rich Shepard
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

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Re: Which dependency list to build first?

Eric Berger
These two pathnames are different

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

Was that your intention?


On Wed, Feb 27, 2019 at 11:45 PM Rich Shepard <[hidden email]>
wrote:

> 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
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

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Re: Which dependency list to build first?

Rich Shepard
On Thu, 28 Feb 2019, Eric Berger wrote:

> These two pathnames are different
>
> /usr/lib/R/library/lib/later/later.so
> /usr/lib/R/library/later.so
>
> Was that your intention?

Eric,

No. I apologize for being imprecise. On this host later.so is located at
only /usr/lib/R/library/later/libs/later.so.

Regards,

Rich

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Re: Which dependency list to build first?

R help mailing list-2
In reply to this post by Rich Shepard
On Tue, 26 Feb 2019 05:47:38 -0800 (PST)
Rich Shepard <[hidden email]> wrote:

> /usr/lib/R/library/later/libs/later.so: undefined symbol:
> __atomic_fetch_add_8

Stackoverflow may help at least in locating the trouble.  A web search
indicates the error is not unknown in other contexts than R.  

JWDougherty

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