Re: [R] Which dependency list to build first?
On Tue, 26 Feb 2019 05:47:38 -0800 (PST) Rich Shepard 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 __ R-help@r-project.org 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.
Re: [R] Which dependency list to build first?
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 __ R-help@r-project.org 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.
Re: [R] Which dependency list to build first?
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 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 > > __ > R-help@r-project.org 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]] __ R-help@r-project.org 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.
Re: [R] Which dependency list to build first?
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 __ R-help@r-project.org 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.
Re: [R] Which dependency list to build first?
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 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 > > __ > R-help@r-project.org 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]] __ R-help@r-project.org 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.
Re: [R] Which dependency list to build first?
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 __ R-help@r-project.org 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.
Re: [R] Which dependency list to build first?
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
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
>
> __
> R-help@r-project.org 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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Which dependency list to build first?
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
__
R-help@r-project.org 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.
Re: [R] Which dependency list to build first?
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
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
>
> __
> R-help@r-project.org 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]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Which dependency list to build first?
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
__
R-help@r-project.org 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.
Re: [R] Which dependency list to build first?
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 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 > > __ > R-help@r-project.org 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]] __ R-help@r-project.org 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.
Re: [R] 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 __ R-help@r-project.org 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.
Re: [R] 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? 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 __ R-help@r-project.org 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.
Re: [R] Which dependency list to build first?
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 __ R-help@r-project.org 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.
Re: [R] Which dependency list to build first?
> 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 > __ > R-help@r-project.org 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. __ R-help@r-project.org 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.
[R] Which dependency list to build first?
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 __ R-help@r-project.org 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.
