[R-pkg-devel] Linking to C library from within R package - library not loaded error

[Satyaprakash Nayak]

Hi

I am trying to develop a package which links against a C library which is
installed on my system (Mac OSX) in the /usr/local/lib directory.

The C library against which I am linking is called 'Sundials
'
(an efficient solver for large scale ordinary differential/algebraic
equations) and the specific error I get when I perform 'clean and rebuild`
in RStudio, I get the following error

Library not loaded: libsundials_nvecserial.0.dylib


The Makevars is as follows

PKG_CPPFLAGS= -I../inst/include/ -I src/sundials
> PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -L/usr/local/lib
> -lsundials_nvecserial -lsundials_cvode -lm


Initially, I was thinking of building the library in the package itself so
that the users don't have to install `sundials` to use the package, but I
have abandoned that approach (for now) and I am now trying to link to the
libraries installed on the system. Currently, the package does not do
anything useful, I am just trying to allocate values to the N_VNew_Serial() (a
vector type defined by the sundials library), see -
https://github.com/sn248/Rcppsbmod/blob/pr/1/src/sundials_test.cpp

I have confirmed that /usr/local/lib does contain
libsundials_nvecserial.0.dylib

The source code for the entire package can be found at -
https://github.com/sn248/Rcppsbmod/tree/pr/1

In the interest of full disclosure, I have asked a similar question before
on StackOverflow also -
http://stackoverflow.com/questions/37819967/compiling-c-in-rcpp-with-external-c-library

and received comments that this is a linking error, not compilation.

To confirm that I have sundials installed and working on my laptop, I tried
to compile and link an example from the library using the command

gcc -Wall cvRoberts_dns.c -o cvRoberts_dns.exe -I/usr/local/include
-L/usr/local/lib/ -lsundials_cvode -lsundials_nvecserial -lm

and was able to run it successfully.

Any help in linking successfully to this library in my package would be
highly appreciated.
Thanks!
SN

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Re: [R-pkg-devel] Linking to C library from within R package - library not loaded error

[Satyaprakash Nayak]

A quick update

The correct command to run the sundials example is

gcc -Wall cvRoberts_dns.c -o cvRoberts_dns.exe -I/usr/local/include
-L/usr/local/lib/ -lsundials_cvode -lsundials_nvecserial -lm

OR

gcc -Wall cvRoberts_dns.c -o cvRoberts_dns.exe
/usr/local/lib/libsundials_cvode.a /usr/local/lib/libsundials_nvecserial.a

also, the command

PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
/usr/local/lib/libsundials_cvode.a /usr/local/lib/libsundials_nvecserial.a

now works! So, linking to a static library works, but linking to the .so or
.dylib does not in this case.

Thanks

SN

On Wed, Jul 6, 2016 at 12:22 PM, Satyaprakash Nayak 
wrote:

> Hi
>
> I am trying to develop a package which links against a C library which is
> installed on my system (Mac OSX) in the /usr/local/lib directory.
>
> The C library against which I am linking is called 'Sundials
> <http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers>'
> (an efficient solver for large scale ordinary differential/algebraic
> equations) and the specific error I get when I perform 'clean and rebuild`
> in RStudio, I get the following error
>
> Library not loaded: libsundials_nvecserial.0.dylib
>
>
> The Makevars is as follows
>
> PKG_CPPFLAGS= -I../inst/include/ -I src/sundials
>> PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -L/usr/local/lib
>> -lsundials_nvecserial -lsundials_cvode -lm
>
>
> Initially, I was thinking of building the library in the package itself so
> that the users don't have to install `sundials` to use the package, but I
> have abandoned that approach (for now) and I am now trying to link to the
> libraries installed on the system. Currently, the package does not do
> anything useful, I am just trying to allocate values to the N_VNew_Serial()
> (a vector type defined by the sundials library), see -
> https://github.com/sn248/Rcppsbmod/blob/pr/1/src/sundials_test.cpp
>
> I have confirmed that /usr/local/lib does contain
> libsundials_nvecserial.0.dylib
>
> The source code for the entire package can be found at -
> https://github.com/sn248/Rcppsbmod/tree/pr/1
>
> In the interest of full disclosure, I have asked a similar question before
> on StackOverflow also -
> http://stackoverflow.com/questions/37819967/compiling-c-in-rcpp-with-external-c-library
>
> and received comments that this is a linking error, not compilation.
>
> To confirm that I have sundials installed and working on my laptop, I
> tried to compile and link an example from the library using the command
>
> gcc -Wall cvRoberts_dns.c -o cvRoberts_dns.exe -I/usr/local/include
> -L/usr/local/lib/ -lsundials_cvode -lsundials_nvecserial -lm
>
> and was able to run it successfully.
>
> Any help in linking successfully to this library in my package would be
> highly appreciated.
> Thanks!
> SN
>
>

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[R-pkg-devel] Can't build package but can load it with devtools::load_all()

[Satyaprakash Nayak]

Hi

I am trying to build a package with interfaces with C library libSBML
<http://sbml.org/Software/libSBML> (although a package libSBML exists).
When I try to build the package using "Clean and Rebuild" command in
RStudio, I am getting the following error

** R
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared object
> '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcppsbml/libs/Rcppsbml.so':
>
> dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcppsbml/libs/Rcppsbml.so,
> 6): Library not loaded: libsbml.5.dylib
>   Referenced from:
> /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcppsbml/libs/Rcppsbml.so
>   Reason: image not found
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcppsbml’
> Exited with status 1.


However, if I issue the command

devtools::load_all()

after "Clean and Rebuild" command, I get the message

Loading Rcppsbml


and I can also use the functions defined in the package! However, as soon
as I restart my R session, I cannot load the library (understandable, as I
don't think the package is built correctly).

Based on the error shown, I think libsbml.5.dylib is not being loaded,
however, it is there in the /usr/local/lib folder.

The code for this package can be found at

https://github.com/sn248/Rcppsbml

Any help in resolving this error would be highly appreciated!

Thank you
Satyaprakash Nayak

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Re: [R-pkg-devel] Can't build package but can load it with devtools::load_all()

[Satyaprakash Nayak]

Just an update - I re-installed libSBML and now

devtools::load_all()


is giving an error

> devtools::load_all()
> Loading Rcppsbml
> Error in dyn.load(dllfile) :
>   unable to load shared object '//Rcppsbml/src/Rcppsbml.so':
>   dlopen(//Rcppsbml/src/Rcppsbml.so, 6): Symbol not found:
> __ZN7libsbml10SBMLReader16readSBMLFromFileERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIc


 is the path to package directory

Thank you
Satyaprakash Nayak

On Sun, Jul 31, 2016 at 11:32 PM, Satyaprakash Nayak 
wrote:

> Hi
>
> I am trying to build a package with interfaces with C library libSBML
> <http://sbml.org/Software/libSBML> (although a package libSBML exists).
> When I try to build the package using "Clean and Rebuild" command in
> RStudio, I am getting the following error
>
> ** R
>> ** preparing package for lazy loading
>> ** help
>> *** installing help indices
>> ** building package indices
>> ** testing if installed package can be loaded
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>   unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcppsbml/libs/Rcppsbml.so':
>>
>> dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcppsbml/libs/Rcppsbml.so,
>> 6): Library not loaded: libsbml.5.dylib
>>   Referenced from:
>> /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcppsbml/libs/Rcppsbml.so
>>   Reason: image not found
>> Error: loading failed
>> Execution halted
>> ERROR: loading failed
>> * removing
>> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcppsbml’
>> Exited with status 1.
>
>
> However, if I issue the command
>
> devtools::load_all()
>
> after "Clean and Rebuild" command, I get the message
>
> Loading Rcppsbml
>
>
> and I can also use the functions defined in the package! However, as soon
> as I restart my R session, I cannot load the library (understandable, as I
> don't think the package is built correctly).
>
> Based on the error shown, I think libsbml.5.dylib is not being loaded,
> however, it is there in the /usr/local/lib folder.
>
> The code for this package can be found at
>
> https://github.com/sn248/Rcppsbml
>
> Any help in resolving this error would be highly appreciated!
>
> Thank you
> Satyaprakash Nayak
>

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[R-pkg-devel] Warnings from upstream C library in CRAN submission

[Satyaprakash Nayak]

Hi

I had a package 'sundialr' which was archived from CRAN. It is an interface
to some of the solvers in SUNDIALS ODE Solving library. I have fixed the
issue which was related to emails being forwarded from the maintainer's
email address.

The repository code can be found at - https://github.com/sn248/sundialr

I have updated the upstream library and now I am getting the following
warnings from CRAN which are all related to the upstream library. The
package compiles without any other issues and can be used.

Flavor: r-devel-windows-x86_64
Check: whether package can be installed, Result: WARNING
  Found the following significant warnings:
./sundials/sundials/sundials_hashmap.h:26:48: warning: conversion from
'long long unsigned int' to 'long unsigned int' changes value from
'14695981039346656037' to '2216829733' [-Woverflow]
./sundials/sundials/sundials_hashmap.h:27:48: warning: conversion from
'long long unsigned int' to 'long unsigned int' changes value from
'1099511628211' to '435' [-Woverflow]
sundials/sundials/sundials_hashmap.h:26:48: warning: conversion from
'long long unsigned int' to 'long unsigned int' changes value from
'14695981039346656037' to '2216829733' [-Woverflow]
sundials/sundials/sundials_hashmap.h:27:48: warning: conversion from
'long long unsigned int' to 'long unsigned int' changes value from
'1099511628211' to '435' [-Woverflow]
sundials/sundials/sundials_profiler.c:71:24: warning: function
declaration isn't a prototype [-Wstrict-prototypes]
  See 'd:/RCompile/CRANincoming/R-devel/sundialr.Rcheck/00install.out' for
details.
  Used C++ compiler: 'g++.exe (GCC) 12.3.0'

Flavor: r-devel-linux-x86_64-debian-gcc
Check: whether package can be installed, Result: WARNING
  Found the following significant warnings:
sundials/sundials/sundials_profiler.c:71:41: warning: a function
declaration without a prototype is deprecated in all versions of C
[-Wstrict-prototypes]
  See '/srv/hornik/tmp/CRAN/sundialr.Rcheck/00install.out' for details.
  Used C++ compiler: 'Debian clang version 17.0.6 (5)'

I am hesitant to change anything in the SUNDIALS library C code because I
don't understand the consequences of changing anything there.

Any help will be kindly appreciated.

Thank you.

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Re: [R-pkg-devel] Warnings from upstream C library in CRAN submission

[Satyaprakash Nayak]

Thank you Jeff and Simon for your feedback.

I have filed your feedback as an issue to the SUNDIALS developers at  -
https://github.com/LLNL/sundials/issues/409

Thank you.

On Sat, Feb 3, 2024 at 10:38 AM Satyaprakash Nayak 
wrote:

> Hi
>
> I had a package 'sundialr' which was archived from CRAN. It is an interface
> to some of the solvers in SUNDIALS ODE Solving library. I have fixed the
> issue which was related to emails being forwarded from the maintainer's
> email address.
>
> The repository code can be found at - https://github.com/sn248/sundialr
>
> I have updated the upstream library and now I am getting the following
> warnings from CRAN which are all related to the upstream library. The
> package compiles without any other issues and can be used.
>
> Flavor: r-devel-windows-x86_64
> Check: whether package can be installed, Result: WARNING
>   Found the following significant warnings:
> ./sundials/sundials/sundials_hashmap.h:26:48: warning: conversion from
> 'long long unsigned int' to 'long unsigned int' changes value from
> '14695981039346656037' to '2216829733' [-Woverflow]
> ./sundials/sundials/sundials_hashmap.h:27:48: warning: conversion from
> 'long long unsigned int' to 'long unsigned int' changes value from
> '1099511628211' to '435' [-Woverflow]
> sundials/sundials/sundials_hashmap.h:26:48: warning: conversion from
> 'long long unsigned int' to 'long unsigned int' changes value from
> '14695981039346656037' to '2216829733' [-Woverflow]
> sundials/sundials/sundials_hashmap.h:27:48: warning: conversion from
> 'long long unsigned int' to 'long unsigned int' changes value from
> '1099511628211' to '435' [-Woverflow]
> sundials/sundials/sundials_profiler.c:71:24: warning: function
> declaration isn't a prototype [-Wstrict-prototypes]
>   See 'd:/RCompile/CRANincoming/R-devel/sundialr.Rcheck/00install.out' for
> details.
>   Used C++ compiler: 'g++.exe (GCC) 12.3.0'
>
> Flavor: r-devel-linux-x86_64-debian-gcc
> Check: whether package can be installed, Result: WARNING
>   Found the following significant warnings:
> sundials/sundials/sundials_profiler.c:71:41: warning: a function
> declaration without a prototype is deprecated in all versions of C
> [-Wstrict-prototypes]
>   See '/srv/hornik/tmp/CRAN/sundialr.Rcheck/00install.out' for details.
>   Used C++ compiler: 'Debian clang version 17.0.6 (5)'
>
> I am hesitant to change anything in the SUNDIALS library C code because I
> don't understand the consequences of changing anything there.
>
> Any help will be kindly appreciated.
>
> Thank you.
>

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Re: [R-pkg-devel] Help with reproducing (and solving) clang-UBSAN and Solaris installation errors

[Satyaprakash Nayak]

Thank you very much Kevin for your response.

I got R development with clang-6.0 working on a Ubuntu machine yesterday so
will investigate this further to see if there is anything more subtle going
on w.r.t. UBSAN issue and report here.

Regarding Solaris, I have code such as

SOURCES = $(cvode.cpp RcppExports.cpp)
OBJECTS = $(SOURCES:.cpp=.o)

Maybe that's causing a problem, I read section 1.6 of R extensions
mentioned

" Commonly misused GNU extensions are conditional inclusions (ifeq and the
like), ${shell ...}, ${wildcard ...} and similar, and the use of +=68
 and :=
. "

I will try with

OBJECTS = cvode.o RcppExports.o

but since, rhub is not giving an error, I am not sure how I can really test
this.

Thanks for your suggestion about

SystemRequirements: GNU make

That may be the final solution for me to get this working on Solaris.

Best
Satya


On Mon, Jul 9, 2018 at 11:48 AM Kevin Ushey  wrote:

> The UBSAN error:
>
> cvode.cpp:58:11: runtime error: call to function
> cv_Roberts_dns(double, Rcpp::Vector<14, Rcpp::PreserveStorage>)
> through pointer to incorrect function type 'Rcpp::Vector<14,
> PreserveStorage> (*)(double, Rcpp::Vector<14, PreserveStorage>)'
>
> /tmp/RtmplnLW4G/sourceCpp-x86_64-pc-linux-gnu-0.12.17/sourcecpp_a916f8734/filea91617630abf.cpp:9:
> note: cv_Roberts_dns(double, Rcpp::Vector<14, Rcpp::PreserveStorage>)
> defined here
> SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior cvode.cpp:58:11 in
>
> sounds like it might be a false positive, since the function
> signatures do appear to be identical. Of course, there may be
> something more subtle going on, but absent any other ill effects I
> think the message can be ignored. For what it's worth, one similar
> false positive is reported here at
> https://github.com/google/sanitizers/issues/911.
>
> The actual compilation error you're seeing on Solaris:
>
> mksh: Fatal error in reader: = missing from replacement macro reference
>
> implies that you're likely trying to use a GNU-ism in your Makefile /
> Makevars. R requires that Makefiles be portable by default, as per
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars
> .
> If you _really_ need the GNU-isms, you can add something like:
>
> SystemRequirements: GNU make
>
> to request that GNU make is used on all platforms your package is built on.
>
> Best,
> Kevin
>
> On Sun, Jul 8, 2018 at 3:53 AM SN248  wrote:
> >
> > Dear all
> >
> > I recently submitted an R package to CRAN which was accepted. However,
> the
> > package is failing additional tests, i.e., it fails to install on Solaris
> > and also produces a clang-UBSAN issue. These can be seen here
> >
> > https://cran.r-project.org/web/checks/check_results_sundialr.html
> >
> > I tried to reproduce the installation error for Solaris and clang-UBSAN
> > issue using rhub (R package). However, in both cases, I don't see any
> error
> > reported by rhub.
> >
> > Solaris installation went fine (Oracle Solaris 10, x86, 32 bit, R-patched
> > (experimental)). See the report below:
> >
> >
> https://builder.r-hub.io/status/original/sundialr_0.1.0.tar.gz-b13f34c036448a13cbc147f4fb2cf37b
> >
> > and
> >
> > No errors were reported when I run 'check_with_sanitizers()' command (I
> > assume that is the right command to generate clang-UBSAN errors, though
> the
> > Platform information is - Debian Linux, R-devel, GCC ASAN/UBSAN). See the
> > report of the test below:
> >
> >
> https://builder.r-hub.io/status/original/sundialr_0.1.0.tar.gz-a38aa86e16494f41b6f2e2e093547b7b
> >
> > I am not sure how to proceed with debugging those errors as I am not able
> > to reproduce them. Is there any way to test installation on Solaris (I
> > don't have access to one, unfortunately) and reproduce clang-UBSAN issue.
> >
> > The clang-UBSAN issue _may_ be related to Rcpp::XPtr and _may_ remain
> > unresolved (based on the thread in Rcpp-devel forum earlier (I could have
> > mis-interpreted the whole discussion there) -
> >
> http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2017-July/009656.html
> > )
> >
> > Any help in how to reproduce these issues will be highly appreciated.
> >
> > On a separate note - in case these issues remain unresolved, is the
> package
> > doomed to go to CRAN archives then? The package installation and running
> > examples went without error/warning/note on all the platforms in rhub.
> >
> > Thanks
> > SN
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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[R-pkg-devel] package fails with parallel make - would forcing a serial version work?

[Satyaprakash Nayak]

Dear R package developers

I published a package on CRAN last year (sundialr) which is now failing
with as it is not make to compile a static library with parallel make.

In this package, I compile a static library (libsundials_all.a) from source
files of a third party. The specifics of compiling the static library can
be found at - https://github.com/sn248/sundialr/blob/master/src/Makevars

Now, I got the following error message from CRAN (actually, I was informed
of this before, but had neglected to fix it). Here is the message from one
of the CRAN maintainers ..

***
This have just failed to install for me with a parallel make:

g++ -std=gnu++98 -std=gnu++98 -shared
-L/data/blackswan/ripley/extras/lib64 -L/usrlocal/lib64 -o sundialr.so
cvode.o RcppExports.o -L/data/blackswan/ripley/R/R-patched/lib -lRlapack
-L/data/blackswan/ripley/R/R-patched/lib -lRblas -lgfortran -lm
-lquadmath -L../inst/ ../inst/libsundials_all.a
g++: error: ../inst/libsundials_all.a: No such file or directory
make[1]: *** [/data/blackswan/ripley/R/R-patched/share/make/shlib.mk:6:
sundialr.so] Error 1
*

It seems the package fails to generate the static library with the parallel
make. The easiest solution I could think of for this problem was to force a
serial version of make using the .NOTPARALLEL phony command in Makevars and
Makevars.win(https://github.com/sn248/sundialr/blob/master/src/Makevars). I
have made this change and it seems to work on my machine and on testing
with TravisCI and Appveyor(https://github.com/sn248/sundialr).

However, before I re-submit to CRAN, I wanted to get an opinion as to will
this be enough to get rid of the error with parallel make?

Any suggestions would be very much appreciated, thank you!
Satyaprakash

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Re: [R-pkg-devel] package fails with parallel make - would forcing a serial version work?

[Satyaprakash Nayak]

Thank you Paul and Avi for your response. Indeed, there was an error in
Makefile which could have been contributing to the issues with parallel
make. I have re-submitted after correcting for the mistakes in Makefile,
hopefully it will not throw errors with parallel make now.

Thank you for your advice.
Satyaprakash


On Mon, Jan 14, 2019 at 2:01 PM Avraham Adler 
wrote:

> If you want to use .NOTPARRALLEL, that’s considered non-portable as it’s
> GNU-make specific, (I got an email from Dr. Ripley this week) so you have
> to add Gnu Make to the system requirements in the DESCRIPTION or find the
> right sequence of targets to ensure order is maintained even in parallel
> make.
>
> Avi
>
> On Mon, Jan 14, 2019 at 1:29 PM Paul Gilbert 
> wrote:
>
>> (I didn't see an answer to this, so ...)
>>
>> I think using .NOTPARALLEL will usually get rid of the error but, in my
>> experience, this problem is usually caused by an incorrect or incomplete
>> Makefile. When not done in parallel this missing target is usually
>> getting done first as a side-affect of something that happens before and
>> usually finishes before it is needed. Your luck does not hold in
>> parallel. The better fix is to correct your Makefile.
>>
>> Paul
>>
>> On 1/10/19 4:54 PM, Satyaprakash Nayak wrote:
>> > Dear R package developers
>> >
>> > I published a package on CRAN last year (sundialr) which is now failing
>> > with as it is not make to compile a static library with parallel make.
>> >
>> > In this package, I compile a static library (libsundials_all.a) from
>> source
>> > files of a third party. The specifics of compiling the static library
>> can
>> > be found at -
>> https://github.com/sn248/sundialr/blob/master/src/Makevars
>> >
>> > Now, I got the following error message from CRAN (actually, I was
>> informed
>> > of this before, but had neglected to fix it). Here is the message from
>> one
>> > of the CRAN maintainers ..
>> >
>> >
>> ***
>> > This have just failed to install for me with a parallel make:
>> >
>> > g++ -std=gnu++98 -std=gnu++98 -shared
>> > -L/data/blackswan/ripley/extras/lib64 -L/usrlocal/lib64 -o sundialr.so
>> > cvode.o RcppExports.o -L/data/blackswan/ripley/R/R-patched/lib -lRlapack
>> > -L/data/blackswan/ripley/R/R-patched/lib -lRblas -lgfortran -lm
>> > -lquadmath -L../inst/ ../inst/libsundials_all.a
>> > g++: error: ../inst/libsundials_all.a: No such file or directory
>> > make[1]: *** [/data/blackswan/ripley/R/R-patched/share/make/shlib.mk:6:
>> > sundialr.so] Error 1
>> >
>> *
>> >
>> > It seems the package fails to generate the static library with the
>> parallel
>> > make. The easiest solution I could think of for this problem was to
>> force a
>> > serial version of make using the .NOTPARALLEL phony command in Makevars
>> and
>> > Makevars.win(https://github.com/sn248/sundialr/blob/master/src/Makevars).
>> I
>> > have made this change and it seems to work on my machine and on testing
>> > with TravisCI and Appveyor(https://github.com/sn248/sundialr).
>> >
>> > However, before I re-submit to CRAN, I wanted to get an opinion as to
>> will
>> > this be enough to get rid of the error with parallel make?
>> >
>> > Any suggestions would be very much appreciated, thank you!
>> > Satyaprakash
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > __
>> > R-package-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> >
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
> --
> Sent from Gmail Mobile
>

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[R-pkg-devel] Creating and hosting static libraries for package installation on Windows

[Satyaprakash Nayak]

Hi r-package-devel

I am working on updating my package `sundialr` (
https://cran.r-project.org/web/packages/sundialr/index.html), wherein I was
earlier bundling the C source files with the package, but now I am using
`cmake` to create static libraries for the upstream C library SUNDIALS
which the package provides an interface for. In brief, the previous
approach can be found at:

https://github.com/sn248/sundialr/blob/master/src/Makevars

And the new approach can be seen below (heavily borrowed from nloptr
package installation approach):

https://github.com/sn248/sundialr/blob/cmake-install/tools/cmake_call.sh

The second approach works successfully on linux and macOS platforms
(checked by rhub).

I am struggling to get this working on a Windows platform, and have looked
at a few packages (e.g., nloptr, rcppredis, openssl) which have solved this
issue. As I understand the following steps are required to get the static
libraries in correct locations for package installation on the Windows

1) Host the .tar.gz files or .zip files on https://github.com/rwinlib/
(deprecated now) or https://github.com/r-windows/bundles/releases/download/
which should contain the static libraries (*.a files) in separate folders
for i386, x64-ucrt and x-64 platforms and required header files in the
`include` folder.

2) Use a winlibs.R file within the `tools` sub-directory in the package
file structure to download the .zip or .tar.gz file and extract them to a
`windows` directory.

3) Set PKG_CPPFLAGS and PKG_LIBS via Makewars.win file in src sub-directory
in the package files.

Currently, I am struggling with Step #1, i.e., how to create the required
.zip or .tar.gz files and host them on
https://github.com/r-windows/bundles/releases for download. I will be
thankful if any one can provide some guidance in this regard.

Sincerely
Satya

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Re: [R-pkg-devel] Creating and hosting static libraries for package installation on Windows

[Satyaprakash Nayak]

For some reason, I am not getting emails from the list, but would like to
thank Uwe and Tomas for their help. The code Tomas has provided in his
response has resolved the issue.

Satya


On Tue, Dec 10, 2024 at 11:23 PM Satyaprakash Nayak 
wrote:

> Hi r-package-devel
>
> I am working on updating my package `sundialr` (
> https://cran.r-project.org/web/packages/sundialr/index.html), wherein I
> was
> earlier bundling the C source files with the package, but now I am using
> `cmake` to create static libraries for the upstream C library SUNDIALS
> which the package provides an interface for. In brief, the previous
> approach can be found at:
>
> https://github.com/sn248/sundialr/blob/master/src/Makevars
>
> And the new approach can be seen below (heavily borrowed from nloptr
> package installation approach):
>
> https://github.com/sn248/sundialr/blob/cmake-install/tools/cmake_call.sh
>
> The second approach works successfully on linux and macOS platforms
> (checked by rhub).
>
> I am struggling to get this working on a Windows platform, and have looked
> at a few packages (e.g., nloptr, rcppredis, openssl) which have solved this
> issue. As I understand the following steps are required to get the static
> libraries in correct locations for package installation on the Windows
>
> 1) Host the .tar.gz files or .zip files on https://github.com/rwinlib/
> (deprecated now) or
> https://github.com/r-windows/bundles/releases/download/
> which should contain the static libraries (*.a files) in separate folders
> for i386, x64-ucrt and x-64 platforms and required header files in the
> `include` folder.
>
> 2) Use a winlibs.R file within the `tools` sub-directory in the package
> file structure to download the .zip or .tar.gz file and extract them to a
> `windows` directory.
>
> 3) Set PKG_CPPFLAGS and PKG_LIBS via Makewars.win file in src sub-directory
> in the package files.
>
> Currently, I am struggling with Step #1, i.e., how to create the required
> .zip or .tar.gz files and host them on
> https://github.com/r-windows/bundles/releases for download. I will be
> thankful if any one can provide some guidance in this regard.
>
> Sincerely
> Satya
>
>

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