On 3 May 2018 at 19:08, Evan Biederstedt wrote:
| Given the R package structure, I was thinking it would be possible to link
| to the C library (not installed with 'sudo make install') via the `-L`
| flag, maybe `-L/something/src/bamdb/build`
This would work if and only if ldconfig exported the (
Hi Dirk
I appreciate the help.
> You have the hardest possibe deployment option here it requires temporary
root to make a library a system library -- and R CMD ... does not have that.
I think I was able to sidestep this.
After installing bamdb without 'sudo make install'/root privileges, I was
On 3 May 2018 at 16:19, Evan Biederstedt wrote:
| Working with Linux first, is it common to compile a C library (i.e. bamdb)
| within /src, and then use extern? My understanding is that I will have to
| change the R package's Makevars to compile the C library first, and then
| link to this.
|
| I
Hi @Keith
Thanks for the help and apologies for the delay. You're correct---when I
change the install name it does work, i.e. use `sudo install_name_tool -id
/usr/local/lib/libbamdb.dylib /usr/local/lib/libbamdb.dylib`
Thanks for this! I hadn't known about `@rpath` in Mac OS, and in retrospect
I
From my experience, R (on macOS) doesn't play well with libraries that have
install names containing runtime search paths. By changing the install name, I
mean changing the '@rpath' part here:
$ otool -L /usr/local/lib/libbamdb.dylib
/usr/local/lib/libbamdb.dylib:
@rpath/libbamdb.dylib
@Dirk
> Could you possibly construct a smaller, self-contained example exhibiting
the
same problem? That may be more efficient than requiring volunteer helpers to
install four other libraries.
Apologies, this is on the to-do list.
@Keith
Thanks for trying this out. This is interesting.
> Worke
Worked for me, after I modified the install name of libbamdb (from a runtime
path to the installation directory, /usr/local/lib/libbamdb.dylib).
* installing to library ‘/Users//R-devel/lib/R/library’
* installing *source* package ‘bambi’ ...
** libs
clang++-mp-6.0 -std=gnu++11 -I"/Users//R-devel
Evan,
Could you possibly construct a smaller, self-contained example exhibiting the
same problem? That may be more efficient than requiring volunteer helpers to
install four other libraries.
Dirk
--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
@Keith
> Unless I'm mistaken, neither are required to install binary packages. Can
you check your *source* build setup; try:
> curl -O https://cran.r-project.org/src/contrib/RcppArmadillo_0.8.
500.0.tar.gz
> R CMD INSTALL RcppArmadillo_0.8.500.0.tar.gz
This looks successful
```
$ R CMD INSTALL
Unless I'm mistaken, neither are required to install binary packages. Can you
check your *source* build setup; try:
curl -O https://cran.r-project.org/src/contrib/RcppArmadillo_0.8.500.0.tar.gz
R CMD INSTALL RcppArmadillo_0.8.500.0.tar.gz
If that goes through without a hitch then it's probably a
I would add, I think clang and gfortran are working correctly, as these are
required for `install.packages('RcppArmadillo')` to install properly.
On Tue, May 1, 2018 at 3:06 AM, Evan Biederstedt wrote:
> Maybe my Mac OS needs updating...possibly something with XCode, but it's
> not clear how...
Maybe my Mac OS needs updating...possibly something with XCode, but it's
not clear how...
--- mac OS Sierra 10.12.6
--- CRAN R 3.4.3
---clang & gfortran
$ clang --version
Apple LLVM version 9.0.0 (clang-900.0.39.2)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir: /Library/D
> Am 30.04.2018 um 23:42 schrieb Evan Biederstedt :
>
> @Ralf
>
> > I had not installed the necessary C library, so unsurprisingly the
> > compilation step already failed. What I find interesting is that in my case
> > "-std=gnu++11“ and "-I../inst/include/" are present in the command line
>
@Ralf
> I had not installed the necessary C library, so unsurprisingly the
compilation step already failed. What I find interesting is that in my case
"-std=gnu++11“ and "-I../inst/include/" are present in the command line
options for clang++. These are also missing from what you quoted and are
al
> Am 30.04.2018 um 21:01 schrieb Evan Biederstedt :
> @Ralf
>
> > You can change the used compiler for *your* system via ~/.R/Makevars,
> > though. From my point of view that is a (short-time) workaround only. You
> > have to figure out why clang does not like your package/library.
>
> I've ye
Evan,
Could something be amiss with your macOS machine? Can you install other
packages without issues on it?
Dirk
--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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Hi all
Thank you for the responses.
@Keith
> Looks like your PKG_LIBS arguments are ignored/overwritten on the Mac
build; ‘bambi.so’ appears to be missing objects contained in -lbamdb, hence
the load error.
Yes, it's odd.
@Dirk
> Are the libraries installed on the macOS box?
When I build ba
On 30 April 2018 at 06:48, Evan Biederstedt wrote:
| Dear list
|
| I have the following R package which is interacting with a C library via
| Rcpp and extern. At some point, the goal is to combine thesebut I'm
| trying this with baby steps.
|
| R package with C++ wrapper:
| https://github.co
Looks like your PKG_LIBS arguments are ignored/overwritten on the Mac build;
‘bambi.so’ appears to be missing objects contained in -lbamdb, hence the load
error.
Keith
> On Apr 30, 2018, at 6:48 AM, Evan Biederstedt
> wrote:
>
> Dear list
>
> I have the following R package which is interact
On 30.04.2018 12:48, Evan Biederstedt wrote:
> How do I direct the Makevars to use g++ and give me the "correct" build
> as I see on Linux? `CXX=g++` or `CXX=/usr/local/bin/g++` doesn't appear
> to work.
Quoting Duncan Murdoch in
https://stat.ethz.ch/pipermail/r-package-devel/2017q4/002087.html:
Dear list
I have the following R package which is interacting with a C library via
Rcpp and extern. At some point, the goal is to combine thesebut I'm
trying this with baby steps.
R package with C++ wrapper:
https://github.com/d-lo/bambi
The C library:
https://github.com/d-lo/bamdb
When I t
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