Hi, We have several projects in the center done by researchers over years in Fortran, there are copy right issues etc to prevent us from giving away the source codes, but a lot of social scientist are interested to use the program. We tried to use dlls to make plugins (available in our website) in various statistics platforms (SAS, STATA and R) to make it available to general public. We used to be able to build R package using dll on version R-2.7.0, , but failed to build with newer R version with the same source. Any help is greatly appreciated. When I try to build R package for newer version of R, I could build to get "lcca_1.0.0.tar.gz", but when I "R CMD check lcca_1.0.0.tar.gz", I got error message as: * using log directory 'D:/project/LCCA/lcca.Rcheck' * using R version 2.15.1 (2012-06-22) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * checking for file 'lcca/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'lcca' version '1.0.0' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... WARNING Found the following executable file(s): libs/lcca.dll Source packages should not contain undeclared executable files. See section 'Package structure' in the 'Writing R Extensions' manual. * checking whether package 'lcca' can be installed ... ERROR Installation failed. See 'D:/project/LCCA/lcca.Rcheck/00install.out' for details. and the message in 00install.out is: * installing *source* package 'lcca' ... ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error in library.dynam(lib, package, package.lib) : DLL 'lcca' not found: maybe not installed for this architecture? Error: loading failed Execution halted ERROR: loading failed * removing 'D:/project/LCCA/lcca.Rcheck/lcca' Thanks a lot! Liy
On 24 August 2012 at 09:06, LIYING HUANG wrote:
| We have several projects in the center done by researchers over years
| in Fortran, there are copy right issues etc to prevent us from
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| giving away the source codes, but a lot of social scientist are
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| interested to use the program. We tried to use dlls to make plugins
| (available in our website) in various statistics platforms
| (SAS, STATA and R) to make it available to general public.
|
| We used to be able to build R package using dll on version R-2.7.0,
| , but failed to build with newer R version with the same source.
| Any help is greatly appreciated.
|
| When I try to build R package for newer version of R, I could build
| to get "lcca_1.0.0.tar.gz", but when I "R CMD check
lcca_1.0.0.tar.gz",
| I got error message as:
|
| * using log directory 'D:/project/LCCA/lcca.Rcheck'
| * using R version 2.15.1 (2012-06-22)
| * using platform: i386-pc-mingw32 (32-bit)
| * using session charset: ISO8859-1
| * checking for file 'lcca/DESCRIPTION' ... OK
| * checking extension type ... Package
| * this is package 'lcca' version '1.0.0'
| * checking package namespace information ... OK
| * checking package dependencies ... OK
| * checking if this is a source package ... OK
| * checking if there is a namespace ... OK
| * checking for executable files ... WARNING
| Found the following executable file(s):
| libs/lcca.dll
| Source packages should not contain undeclared executable files.
| See section 'Package structure' in the 'Writing R Extensions'
manual.
| * checking whether package 'lcca' can be installed ... ERROR
This tells you that in order to have a proper package, you need to include
the very source code you want to hide.
This is a CRAN Policy decision enforced by current R versions (but not the
rather old version you compared against), and there is now way around it.
You could try to construct "defunct" packages lacking the DLLs and
instruct
the users to get them from somewhere else, but that is at the same rather
error prone (as you will lack all the built-time checks you would have with
source code, as well as a better assurrance that compatible tools are used)
and distasteful as CRAN is about Open Source.
So your best bet may be to go back to the copyright holders....
Dirk
--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
You need to setup a Makevars.win and at lest modify PKG_LIBS and probably PKG_FFLAGS PKG_CFLAGS depending on how you link to the DLL. I suggest downloading example packages from Bioc / CRAN to look at. Kasper On Fri, Aug 24, 2012 at 9:06 AM, LIYING HUANG <lxh37@psu.edu> wrote:> > Hi, > > We have several projects in the center done by researchers over years > in Fortran, there are copy right issues etc to prevent us from > giving away the source codes, but a lot of social scientist are > interested to use the program. We tried to use dlls to make plugins > (available in our website) in various statistics platforms > (SAS, STATA and R) to make it available to general public. > > We used to be able to build R package using dll on version R-2.7.0, > , but failed to build with newer R version with the same source. > Any help is greatly appreciated. > > When I try to build R package for newer version of R, I could build > to get "lcca_1.0.0.tar.gz", but when I "R CMD check lcca_1.0.0.tar.gz", > I got error message as: > > * using log directory 'D:/project/LCCA/lcca.Rcheck' > * using R version 2.15.1 (2012-06-22) > * using platform: i386-pc-mingw32 (32-bit) > * using session charset: ISO8859-1 > * checking for file 'lcca/DESCRIPTION' ... OK > * checking extension type ... Package > * this is package 'lcca' version '1.0.0' > * checking package namespace information ... OK > * checking package dependencies ... OK > * checking if this is a source package ... OK > * checking if there is a namespace ... OK > * checking for executable files ... WARNING > Found the following executable file(s): > libs/lcca.dll > Source packages should not contain undeclared executable files. > See section 'Package structure' in the 'Writing R Extensions' manual. > * checking whether package 'lcca' can be installed ... ERROR > Installation failed. > See 'D:/project/LCCA/lcca.Rcheck/00install.out' for details. > > and the message in 00install.out is: > > * installing *source* package 'lcca' ... > ** R > ** data > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > Error in library.dynam(lib, package, package.lib) : > DLL 'lcca' not found: maybe not installed for this architecture? > Error: loading failed > Execution halted > ERROR: loading failed > * removing 'D:/project/LCCA/lcca.Rcheck/lcca' > > > Thanks a lot! > Liy > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >[[alternative HTML version deleted]]
Thanks a lot for those examples, is there any example with Fortran source codes which could depend on an external Fortran DLL? Liy ----- ???? ----- ???: "Berend Hasselman" <bhh at xs4all.nl> ???: "LIYING HUANG" <lxh37 at psu.edu> ??: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>, r-devel at r-project.org ????: ???, 2012? 8 ? 28? ?? 7:02:02 ??: Re: [Rd] include dll in R-package On 28-08-2012, at 01:29, LIYING HUANG wrote:> > I am quite new in R, I looked at R manual- how to build R Package, > still not very clear. Yes, it would be very helpful if I could > download a package having Fortran source codes to look at, Do > you know any package built with Fortran source code? Thanks! >To mention a few: deSolve minpack.lm nleqslv rootSolve xts and probably many more. Berend
One very simple question, probably not appropriate to post this to rdevel list, I put all Fortran files in src, when I do R CMD check, it tries to compile the files by alphabetical order. I tried to modify Makevar, but no luck after staring at the manual for hours. It seems that I could use R CMD SHLIB as following to compile the codes first to get around this problem before doing "R CMD check", but I am curious how to specify the file compilation order in Makevar? Thanks! R CMD SHLIB -o lcca.dll error_handler.f90 constants.f90 Liy ----- Original Message ----- From: "Berend Hasselman" <bhh at xs4all.nl> To: "LIYING HUANG" <lxh37 at psu.edu> Cc: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>, r-devel at r-project.org Sent: Tuesday, August 28, 2012 7:02:02 AM Subject: Re: [Rd] include dll in R-package On 28-08-2012, at 01:29, LIYING HUANG wrote:> > I am quite new in R, I looked at R manual- how to build R Package, > still not very clear. Yes, it would be very helpful if I could > download a package having Fortran source codes to look at, Do > you know any package built with Fortran source code? Thanks! >To mention a few: deSolve minpack.lm nleqslv rootSolve xts and probably many more. Berend
On 30/08/2012 16:59, LIYING HUANG wrote:> > > One very simple question, probably not appropriate to post this to rdevel list, > I put all Fortran files in src, when I do R CMD check, it tries to compile > the files by alphabetical order. I tried to modify Makevar, but no luck > after staring at the manual for hours. It seems that I could use R CMD SHLIB > as following to compile the codes first to get around this problem before > doing "R CMD check", but I am curious how to specify the file compilation order > in Makevar? Thanks!Well, it is in the manual you stared at .... However, for Fortran the order of compilation never matters. If you have Fortran90 modules, it may and that is why Makefiles can have dependencies. 1) You can set OBJECTS to set the order. 2) To avoid problems with parallel makes you should set dependencies, e.g. constants.o: error_handler.o or more likely some module file. Beyond that, R-devel is indeed not the place for a tutorial on Makefiles and compilation.> > R CMD SHLIB -o lcca.dll error_handler.f90 constants.f90 > > Liy > > ----- Original Message ----- > From: "Berend Hasselman" <bhh at xs4all.nl> > To: "LIYING HUANG" <lxh37 at psu.edu> > Cc: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>, r-devel at r-project.org > Sent: Tuesday, August 28, 2012 7:02:02 AM > Subject: Re: [Rd] include dll in R-package > > > On 28-08-2012, at 01:29, LIYING HUANG wrote: > >> >> I am quite new in R, I looked at R manual- how to build R Package, >> still not very clear. Yes, it would be very helpful if I could >> download a package having Fortran source codes to look at, Do >> you know any package built with Fortran source code? Thanks! >> > > To mention a few: > > deSolve > minpack.lm > nleqslv > rootSolve > xts > > and probably many more. > > Berend > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
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