On 5/13/21 7:29 AM, Sokol Serguei wrote:
Le 13/05/2021 à 07:06, SN248 a écrit :
I am working on a package which provides an interface to the libsbml C++
library (http://sbml.org/Software/libSBML) in R. The source code of this
package (r2sbml) can be found at the following link
https://github.com/sn248/r2sbml
The package passes CRAN checks with `R CMD check` on my machine, but
I do
have dependency (libsbml library) installed on my machine (OSX) with
headers and static libs at the usual locations, i.e., /usr/local/include
and /usr/local/lib. The package also passes CRAN check on a Windows
machine
with libsbml installed using Rtools40 and msys2. The DESCRIPTION file
lists
libsbml in SystemRequirements but `R CMD check` obviously fails on rhub
machines because there are no instructions to install libsbml first.
As I
understand, I have the following options to pass checks on CRAN
1. Bundle the source code of libsbml into the package and make the
static
libs on the fly. I don't really want to try this approach even though I
have used this approach before in another package as I think creating
the
static lib is not as straightforward for this library because of the
large
number of files and complex dependency chart.
2. Include header files in the `inst` folder and pull the static libs
from
rwinlib github (assuming the libs can be posted there). I am not sure if
this approach will work on all platforms on which CRAN checks take
place.
3. Somehow include instructions to install libsbml on CRAN machines
(I have
no idea how to do this), or request CRAN maintainers to install libsbml
with header files and libs at usual locations (i.e.,
/usr/local/include and
/usr/local/lib).
I faced the same problem for my package r2sundials and in the end, I
have opted for including the third-party source code into the package.
However, a CRAN team member told me later that such kind of request
(i.e. install third-party software on CRAN machines) can be sent to
the CRAN team. Not sure that they accept but I think you can start by
asking it and if the request is rejected, you can try other options.
I think that sundials is a good example why trying the other options
first is a good suggestion. It is now included in three CRAN packages
(paropt, r2sundials, sundialr). Apart from the duplication (build time),
it has a problem of multiply defined symbols (tentative definitions,
issues with -fno-common, which is the default in GCC 10), which now has
to be handled in the three packages separately.
Best
Tomas
Best,
Serguei.
I am sure some version of this question has been asked before as
there are
many packages which interface with C/C++ libraries listed as
SystemRequirements, but I could not find a clear answer to this aspect,
i.e., passing checks on CRAN machines.
Any guidance here and pros/cons of the above mentioned approaches
will be
very helpful.
Thanks
Satya
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