Re: [R-pkg-devel] package fails with parallel make - would forcing a serial version work?
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 > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package fails with parallel make - would forcing a serial version work?
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 [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package fails with parallel make - would forcing a serial version work?
(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
[R-pkg-devel] package fails with parallel make - would forcing a serial version work?
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
