[Rcpp-devel] Rcpp + Package -> undefined symbol

[Michaël BENESTY]

Hi,

I am trying to wrap the Fasttext lib from Facebook on R.
I have wrote a minimal code based on Rcpp.package.skeleton(module = TRUE)

The C++ file compiles/works with sourceCpp() but it crashes when
building a package.
I have checked many D. Eddelbuettel to get a clue of what to do but no luck.
I have already setup a Makevars file with a path to the include folder.

The package source code is available there:
https://github.com/pommedeterresautee/FastRText

My Makevars:
CXX_STD = CXX11
ROOT_INCLUDE = ../inst/include/
PKG_CPPFLAGS=-I$(ROOT_INCLUDE)


The error I am seeing:
==> R CMD INSTALL --preclean --no-multiarch --with-keep.source FastRText
...
Error: package or namespace load failed for ‘FastRText’ in
dyn.load(file, DLLpath = DLLpath, ...):
impossible de charger l'objet partagé
'/home/geantvert/R/x86_64-pc-linux-gnu-library/3.4/FastRText/libs/FastRText.so':
/home/geantvert/R/x86_64-pc-linux-gnu-library/3.4/FastRText/libs/FastRText.so:
undefined symbol: _ZN8fasttext8FastTextC1Ev


The full log is available there:
https://github.com/pommedeterresautee/FastRText/issues/1

According to c++filt
undefined symbol: _ZN8fasttext8FastTextC1Ev means ->
fasttext::FastText::FastText()


Has anyone an idea?

Kind regards,
Michaël
________________
Michaël BENESTY
***@benesty.fr
Please do not print this e-mail unless you really need to.

[Dirk Eddelbuettel]

On 2 August 2017 at 20:22, Michaël BENESTY wrote:
| Hi,
|
| I am trying to wrap the Fasttext lib from Facebook on R.
| I have wrote a minimal code based on Rcpp.package.skeleton(module = TRUE)
|
| The C++ file compiles/works with sourceCpp() but it crashes when
| building a package.
| I have checked many D. Eddelbuettel to get a clue of what to do but no luck.
| I have already setup a Makevars file with a path to the include folder.
|
| The package source code is available there:
| https://github.com/pommedeterresautee/FastRText
|
| My Makevars:
| CXX_STD = CXX11
| ROOT_INCLUDE = ../inst/include/
| PKG_CPPFLAGS=-I$(ROOT_INCLUDE)

If this is a library then you need to __link__ to it as well. That is
commonly done via PKG_LIBS=... and it may get you the additional problem of
having to ensure users of your package have the fastText library installed.

Dirk
|
|
| The error I am seeing:
| ==> R CMD INSTALL --preclean --no-multiarch --with-keep.source FastRText
| ...
| Error: package or namespace load failed for ‘FastRText’ in
| dyn.load(file, DLLpath = DLLpath, ...):
| impossible de charger l'objet partagé
| '/home/geantvert/R/x86_64-pc-linux-gnu-library/3.4/FastRText/libs/FastRText.so':
| /home/geantvert/R/x86_64-pc-linux-gnu-library/3.4/FastRText/libs/FastRText.so:
| undefined symbol: _ZN8fasttext8FastTextC1Ev
|
|
| The full log is available there:
| https://github.com/pommedeterresautee/FastRText/issues/1
|
| According to c++filt
| undefined symbol: _ZN8fasttext8FastTextC1Ev means ->
| fasttext::FastText::FastText()
|
|
| Has anyone an idea?
|
| Kind regards,
| Michaël
| ________________
| Michaël BENESTY
| ***@benesty.fr
| Please do not print this e-mail unless you really need to.
| _______________________________________________
| Rcpp-devel mailing list
| Rcpp-***@lists.r-forge.r-project.org
| https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel

[Michaël BENESTY]

Thank you Dirk for this answer.

The source code of Fasttext is already embedded in the package (it is
the content of ../inst/include/ and is linked with PKG_CPPFLAGS +
include of headers).
So no issue with user having it or needing to link with PKG_LIBS.

I have checked the compilation with this Makevars:
CXX_STD = CXX11
ROOT_INCLUDE = ../inst/include/
PKG_CPPFLAGS = -I$(ROOT_INCLUDE)
PKG_LIBS = -L$(ROOT_INCLUDE)

And I still get the same error.


Is there anything else to check?
The error seems related to a shared object, do I have something special to do?
I am not even sure to understand the error message, why it can't load
the object if it has compiled?

Kind regards,
Michaël

Post by Dirk Eddelbuettel
| Hi,
|
| I am trying to wrap the Fasttext lib from Facebook on R.
| I have wrote a minimal code based on Rcpp.package.skeleton(module = TRUE)
|
| The C++ file compiles/works with sourceCpp() but it crashes when
| building a package.
| I have checked many D. Eddelbuettel to get a clue of what to do but no luck.
| I have already setup a Makevars file with a path to the include folder.
|
| https://github.com/pommedeterresautee/FastRText
|
| CXX_STD = CXX11
| ROOT_INCLUDE = ../inst/include/
| PKG_CPPFLAGS=-I$(ROOT_INCLUDE)
If this is a library then you need to __link__ to it as well. That is
commonly done via PKG_LIBS=... and it may get you the additional problem of
having to ensure users of your package have the fastText library installed.
Dirk
|
|
| ==> R CMD INSTALL --preclean --no-multiarch --with-keep.source FastRText
| ...
| Error: package or namespace load failed for ‘FastRText’ in
| impossible de charger l'objet partagé
| undefined symbol: _ZN8fasttext8FastTextC1Ev
|
|
| https://github.com/pommedeterresautee/FastRText/issues/1
|
| According to c++filt
| undefined symbol: _ZN8fasttext8FastTextC1Ev means ->
| fasttext::FastText::FastText()
|
|
| Has anyone an idea?
|
| Kind regards,
| Michaël
| ________________
| Michaël BENESTY
| Please do not print this e-mail unless you really need to.
| _______________________________________________
| Rcpp-devel mailing list
| https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
--

[Dirk Eddelbuettel]

On 2 August 2017 at 21:02, Michaël BENESTY wrote:
| Thank you Dirk for this answer.
|
| The source code of Fasttext is already embedded in the package (it is
| the content of ../inst/include/ and is linked with PKG_CPPFLAGS +
| include of headers).
| So no issue with user having it or needing to link with PKG_LIBS.
|
| I have checked the compilation with this Makevars:
| CXX_STD = CXX11
| ROOT_INCLUDE = ../inst/include/
| PKG_CPPFLAGS = -I$(ROOT_INCLUDE)
| PKG_LIBS = -L$(ROOT_INCLUDE)
|
| And I still get the same error.
|
|
| Is there anything else to check?
| The error seems related to a shared object, do I have something special to do?
| I am not even sure to understand the error message, why it can't load
| the object if it has compiled?

Pardon for me being blunt, but you still appear to be confused.

Simply copying headers _and source files_ into inst/include/ does not
magically create a library. You are, from the looks of it, simply not fully
aware of what exactly building a package _against an external library_ needs.

So you need to learn this.

Resist the urge to immediately reply to this email, but rather try to read up
and study some more package. Most of mine use _external_ libraries (not
embedded and built on default) but eg the older RcppMLPACK (by KK) is a
working example (cf https://github.com/rcppmlpack/RcppMLPACK1) as are several
of Jeroen's packages (eg https://github.com/ropensci/hunspell/ as one
semi-random pick).

Dirk

| Kind regards,
| Michaël
|
|
| On Wed, Aug 2, 2017 at 8:32 PM, Dirk Eddelbuettel <***@debian.org> wrote:
| >
| > On 2 August 2017 at 20:22, Michaël BENESTY wrote:
| > | Hi,
| > |
| > | I am trying to wrap the Fasttext lib from Facebook on R.
| > | I have wrote a minimal code based on Rcpp.package.skeleton(module = TRUE)
| > |
| > | The C++ file compiles/works with sourceCpp() but it crashes when
| > | building a package.
| > | I have checked many D. Eddelbuettel to get a clue of what to do but no luck.
| > | I have already setup a Makevars file with a path to the include folder.
| > |
| > | The package source code is available there:
| > | https://github.com/pommedeterresautee/FastRText
| > |
| > | My Makevars:
| > | CXX_STD = CXX11
| > | ROOT_INCLUDE = ../inst/include/
| > | PKG_CPPFLAGS=-I$(ROOT_INCLUDE)
| >
| > If this is a library then you need to __link__ to it as well. That is
| > commonly done via PKG_LIBS=... and it may get you the additional problem of
| > having to ensure users of your package have the fastText library installed.
| >
| > Dirk
| > |
| > |
| > | The error I am seeing:
| > | ==> R CMD INSTALL --preclean --no-multiarch --with-keep.source FastRText
| > | ...
| > | Error: package or namespace load failed for ‘FastRText’ in
| > | dyn.load(file, DLLpath = DLLpath, ...):
| > | impossible de charger l'objet partagé
| > | '/home/geantvert/R/x86_64-pc-linux-gnu-library/3.4/FastRText/libs/FastRText.so':
| > | /home/geantvert/R/x86_64-pc-linux-gnu-library/3.4/FastRText/libs/FastRText.so:
| > | undefined symbol: _ZN8fasttext8FastTextC1Ev
| > |
| > |
| > | The full log is available there:
| > | https://github.com/pommedeterresautee/FastRText/issues/1
| > |
| > | According to c++filt
| > | undefined symbol: _ZN8fasttext8FastTextC1Ev means ->
| > | fasttext::FastText::FastText()
| > |
| > |
| > | Has anyone an idea?
| > |
| > | Kind regards,
| > | Michaël
| > | ________________
| > | Michaël BENESTY
| > | ***@benesty.fr
| > | Please do not print this e-mail unless you really need to.
| > | _______________________________________________
| > | Rcpp-devel mailing list
| > | Rcpp-***@lists.r-forge.r-project.org
| > | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
| > --
| > http://dirk.eddelbuettel.com | @eddelbuettel | ***@debian.org

[Qiang Kou]

Hi, Michael,

All the ".cc" files need to be compiled to make your package work. Putting
them in the inst/include folder is not enough.

I made some quick changes in your package and please check the attachment.

Best,

Qiang Kou

Post by Michaël BENESTY
Hi,
I am trying to wrap the Fasttext lib from Facebook on R.
I have wrote a minimal code based on Rcpp.package.skeleton(module = TRUE)
The C++ file compiles/works with sourceCpp() but it crashes when
building a package.
I have checked many D. Eddelbuettel to get a clue of what to do but no luck.
I have already setup a Makevars file with a path to the include folder.
https://github.com/pommedeterresautee/FastRText
CXX_STD = CXX11
ROOT_INCLUDE = ../inst/include/
PKG_CPPFLAGS=-I$(ROOT_INCLUDE)
==> R CMD INSTALL --preclean --no-multiarch --with-keep.source FastRText
...
Error: package or namespace load failed for ‘FastRText’ in
impossible de charger l'objet partagé
'/home/geantvert/R/x86_64-pc-linux-gnu-library/3.4/
/home/geantvert/R/x86_64-pc-linux-gnu-library/3.4/
undefined symbol: _ZN8fasttext8FastTextC1Ev
https://github.com/pommedeterresautee/FastRText/issues/1
According to c++filt
undefined symbol: _ZN8fasttext8FastTextC1Ev means ->
fasttext::FastText::FastText()
Has anyone an idea?
Kind regards,
Michaël
________________
Michaël BENESTY
Please do not print this e-mail unless you really need to.
_______________________________________________
Rcpp-devel mailing list
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel

[Michaël BENESTY]

Thank you a lot Mr. Kou.
The package is now compiling and I have updated it to load modules at
loading of the package (was quite tricky).
Just to understand, the .cc has compiled just because you moved them
in src/ folder, am I right?
The -I flag in Makevars was not enough?

Kind regards,
Michaël
________________
Michaël BENESTY
***@benesty.fr
Please do not print this e-mail unless you really need to.

Post by Qiang Kou
Hi, Michael,
All the ".cc" files need to be compiled to make your package work. Putting
them in the inst/include folder is not enough.
I made some quick changes in your package and please check the attachment.
Best,
Qiang Kou

Post by Michaël BENESTY
Hi,
I am trying to wrap the Fasttext lib from Facebook on R.
I have wrote a minimal code based on Rcpp.package.skeleton(module = TRUE)
The C++ file compiles/works with sourceCpp() but it crashes when
building a package.
I have checked many D. Eddelbuettel to get a clue of what to do but no luck.
I have already setup a Makevars file with a path to the include folder.
https://github.com/pommedeterresautee/FastRText
CXX_STD = CXX11
ROOT_INCLUDE = ../inst/include/
PKG_CPPFLAGS=-I$(ROOT_INCLUDE)
==> R CMD INSTALL --preclean --no-multiarch --with-keep.source FastRText
...
Error: package or namespace load failed for ‘FastRText’ in
impossible de charger l'objet partagé
undefined symbol: _ZN8fasttext8FastTextC1Ev
https://github.com/pommedeterresautee/FastRText/issues/1
According to c++filt
undefined symbol: _ZN8fasttext8FastTextC1Ev means ->
fasttext::FastText::FastText()
Has anyone an idea?
Kind regards,
Michaël
________________
Michaël BENESTY
Please do not print this e-mail unless you really need to.
_______________________________________________
Rcpp-devel mailing list
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel

--
Qiang Kou
School of Informatics and Computing, Indiana University

[Sokol Serguei]

Michaël Benesty has written at Wed, 2 Aug 2017 23:26:26 +0200

Post by Michaël BENESTY
Thank you a lot Mr. Kou.
The package is now compiling and I have updated it to load modules at
loading of the package (was quite tricky).
Just to understand, the .cc has compiled just because you moved them
in src/ folder, am I right?

Besides compilation issue, it is generally a bad idea to put sources in
inst/ tree.
Because everything in inst/ is installed when binary installation is
requested.
So someone wishing only binaries (let say for the sake of disk space)
will drag
also the sources. A notorious exception to this rule are header only
packages,
like BH. But as far as I understand it is not your case, right?

Serguei.