[R-pkg-devel] Trying to compile R-3.5.1 with openblas for windows
Hello! I'm building a package that needs Openblas for matrix manipulation speed up. I built Openblas on Windows 10. I updated the MkRules.local, src/extra/blas/Makefile.win, etc. Things are working with "make all". However, when I run "make recommended", I have trouble with the Matrix package build. The components of the Cholesky all appear as unreferenced. Has anyone else run into this, please? I'm working with R-3.5.1 source. Thanks, Erin Erin Hodgess, PhD mailto: erinm.hodg...@gmail.com [[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] Trying to compile R-3.5.1 with openblas for windows
Try following the directions here. They have worked for me for years. Please see the comments too. https://www.avrahamadler.com/r-tips/build-openblas-for-windows-r64/ Hope that helps, Avi On Fri, Sep 14, 2018 at 2:34 PM Erin Hodgess wrote: > Hello! > > I'm building a package that needs Openblas for matrix manipulation speed > up. > > I built Openblas on Windows 10. I updated the MkRules.local, > src/extra/blas/Makefile.win, etc. Things are working with "make all". > > However, when I run "make recommended", I have trouble with the Matrix > package build. The components of the Cholesky all appear as unreferenced. > > Has anyone else run into this, please? I'm working with R-3.5.1 source. > > Thanks, > Erin > > Erin Hodgess, PhD > mailto: erinm.hodg...@gmail.com > > [[alternative HTML version deleted]] > > __ > 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] Trying to compile R-3.5.1 with openblas for windows
Hi again! I checked everything, did "make distribution" and the same thing occurred. d:/Rtools/mingw_64/bin/ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o D:\Rtools\mingw_64\bin\nm.exe: 'sublibs': No such file d:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Matrix.dll tmp.def CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o -LD:/erinm/R-3.5.1/bin/x64 -lRlapack -LD:/erinm/R-3.5.1/bin/x64 -lRblas -LD:/erinm/R-3.5.1/extsoft/lib/x64 -LD:/erinm/R-3.5.1/extsoft/lib -LD:/erinm/R-3.5.1/bin/x64 -lR CHMfactor.o:CHMfactor.c:(.text+0x3b): undefined reference to `cholmod_copy_factor' CHMfactor.o:CHMfactor.c:(.text+0x7b): undefined reference to `cholmod_change_factor' CHMfactor.o:CHMfactor.c:(.text+0x92): undefined reference to `cholmod_factor_to_sparse' CHMfactor.o:CHMfactor.c:(.text+0xa5): undefined reference to `cholmod_free_factor' CHMfactor.o:CHMfactor.c:(.text+0x18e): undefined reference to `cholmod_solve' CHMfactor.o:CHMfactor.c:(.text+0x267): undefined reference to `cholmod_copy_factor' CHMfactor.o:CHMfactor.c:(.text+0x27e): undefined reference to `cholmod_updown' CHMfactor.o:CHMfactor.c:(.text+0x396): undefined reference to `cholmod_spsolve' CHMfactor.o:CHMfactor.c:(.text+0x620): undefined reference to `cholmod_factorize_p' CHMfactor.o:CHMfactor.c:(.text+0x658): undefined reference to `cholmod_change_factor' CHMfactor.o:CHMfactor.c:(.text+0x720): undefined reference to `cholmod_copy_factor' CHMfactor.o:CHMfactor.c:(.text+0x87b): undefined reference to `cholmod_copy_factor' CHMfactor.o:CHMfactor.c:(.text+0x8c3): undefined reference to `cholmod_free_factor' Csparse.o:Csparse.c:(.text+0x9f1): undefined reference to `cholmod_sparse_to_dense' Csparse.o:Csparse.c:(.text+0xcd6): undefined reference to `cholmod_speye' Csparse.o:Csparse.c:(.text+0xd21): undefined reference to `cholmod_add' Csparse.o:Csparse.c:(.text+0xd31): undefined reference to `cholmod_free_sparse' Csparse.o:Csparse.c:(.text+0xd3d): undefined reference to `cholmod_copy_sparse' Csparse.o:Csparse.c:(.text+0xd4c): undefined reference to `cholmod_free_sparse' Csparse.o:Csparse.c:(.text+0xdf9): undefined reference to `cholmod_copy' Does this look familiar, please? Thanks, Erin Erin Hodgess, PhD mailto: erinm.hodg...@gmail.com On Fri, Sep 14, 2018 at 1:13 PM Avraham Adler wrote: > Try following the directions here. They have worked for me for years. > Please see the comments too. > > https://www.avrahamadler.com/r-tips/build-openblas-for-windows-r64/ > > Hope that helps, > > Avi > > On Fri, Sep 14, 2018 at 2:34 PM Erin Hodgess > wrote: > >> Hello! >> >> I'm building a package that needs Openblas for matrix manipulation speed >> up. >> >> I built Openblas on Windows 10. I updated the MkRules.local, >> src/extra/blas/Makefile.win, etc. Things are working with "make all". >> >> However, when I run "make recommended", I have trouble with the Matrix >> package build. The components of the Cholesky all appear as unreferenced. >> >> Has anyone else run into this, please? I'm working with R-3.5.1 source. >> >> Thanks, >> Erin >> >> Erin Hodgess, PhD >> mailto: erinm.hodg...@gmail.com >> >> [[alternative HTML version deleted]] >> >> __ >> 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] Trying to compile R-3.5.1 with openblas for windows
No, I’m sorry, I haven’t seen that and I built R 3.5.1 with OpenBLAS recently. Does it work if you use the vanilla BLAS? Avi On Fri, Sep 14, 2018 at 4:14 PM Erin Hodgess wrote: > Hi again! > > I checked everything, did "make distribution" and the same thing occurred. > > > d:/Rtools/mingw_64/bin/ar -rucs ../SuiteSparse_config.a > SuiteSparse_config.o > D:\Rtools\mingw_64\bin\nm.exe: 'sublibs': No such file > d:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Matrix.dll tmp.def > CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o > cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o > dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o > dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o > abIndex.o -LD:/erinm/R-3.5.1/bin/x64 -lRlapack -LD:/erinm/R-3.5.1/bin/x64 > -lRblas -LD:/erinm/R-3.5.1/extsoft/lib/x64 -LD:/erinm/R-3.5.1/extsoft/lib > -LD:/erinm/R-3.5.1/bin/x64 -lR > CHMfactor.o:CHMfactor.c:(.text+0x3b): undefined reference to > `cholmod_copy_factor' > CHMfactor.o:CHMfactor.c:(.text+0x7b): undefined reference to > `cholmod_change_factor' > CHMfactor.o:CHMfactor.c:(.text+0x92): undefined reference to > `cholmod_factor_to_sparse' > CHMfactor.o:CHMfactor.c:(.text+0xa5): undefined reference to > `cholmod_free_factor' > CHMfactor.o:CHMfactor.c:(.text+0x18e): undefined reference to > `cholmod_solve' > CHMfactor.o:CHMfactor.c:(.text+0x267): undefined reference to > `cholmod_copy_factor' > CHMfactor.o:CHMfactor.c:(.text+0x27e): undefined reference to > `cholmod_updown' > CHMfactor.o:CHMfactor.c:(.text+0x396): undefined reference to > `cholmod_spsolve' > CHMfactor.o:CHMfactor.c:(.text+0x620): undefined reference to > `cholmod_factorize_p' > CHMfactor.o:CHMfactor.c:(.text+0x658): undefined reference to > `cholmod_change_factor' > CHMfactor.o:CHMfactor.c:(.text+0x720): undefined reference to > `cholmod_copy_factor' > CHMfactor.o:CHMfactor.c:(.text+0x87b): undefined reference to > `cholmod_copy_factor' > CHMfactor.o:CHMfactor.c:(.text+0x8c3): undefined reference to > `cholmod_free_factor' > Csparse.o:Csparse.c:(.text+0x9f1): undefined reference to > `cholmod_sparse_to_dense' > Csparse.o:Csparse.c:(.text+0xcd6): undefined reference to `cholmod_speye' > Csparse.o:Csparse.c:(.text+0xd21): undefined reference to `cholmod_add' > Csparse.o:Csparse.c:(.text+0xd31): undefined reference to > `cholmod_free_sparse' > Csparse.o:Csparse.c:(.text+0xd3d): undefined reference to > `cholmod_copy_sparse' > Csparse.o:Csparse.c:(.text+0xd4c): undefined reference to > `cholmod_free_sparse' > Csparse.o:Csparse.c:(.text+0xdf9): undefined reference to `cholmod_copy' > > Does this look familiar, please? > > Thanks, > Erin > > Erin Hodgess, PhD > mailto: erinm.hodg...@gmail.com > > > On Fri, Sep 14, 2018 at 1:13 PM Avraham Adler > wrote: > >> Try following the directions here. They have worked for me for years. >> Please see the comments too. >> >> https://www.avrahamadler.com/r-tips/build-openblas-for-windows-r64/ >> >> Hope that helps, >> >> Avi >> >> On Fri, Sep 14, 2018 at 2:34 PM Erin Hodgess >> wrote: >> >>> Hello! >>> >>> I'm building a package that needs Openblas for matrix manipulation speed >>> up. >>> >>> I built Openblas on Windows 10. I updated the MkRules.local, >>> src/extra/blas/Makefile.win, etc. Things are working with "make all". >>> >>> However, when I run "make recommended", I have trouble with the Matrix >>> package build. The components of the Cholesky all appear as >>> unreferenced. >>> >>> Has anyone else run into this, please? I'm working with R-3.5.1 source. >>> >>> Thanks, >>> Erin >>> >>> Erin Hodgess, PhD >>> mailto: erinm.hodg...@gmail.com >>> >>> [[alternative HTML version deleted]] >>> >>> __ >>> R-package-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel >>> >> -- >> Sent from Gmail Mobile >> > -- 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] Trying to compile R-3.5.1 with openblas for windows
That is my next thing to try. Thanks for your help! Erin Hodgess, PhD mailto: erinm.hodg...@gmail.com On Fri, Sep 14, 2018 at 2:46 PM Avraham Adler wrote: > No, I’m sorry, I haven’t seen that and I built R 3.5.1 with OpenBLAS > recently. Does it work if you use the vanilla BLAS? > > Avi > > On Fri, Sep 14, 2018 at 4:14 PM Erin Hodgess > wrote: > >> Hi again! >> >> I checked everything, did "make distribution" and the same thing occurred. >> >> >> d:/Rtools/mingw_64/bin/ar -rucs ../SuiteSparse_config.a >> SuiteSparse_config.o >> D:\Rtools\mingw_64\bin\nm.exe: 'sublibs': No such file >> d:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Matrix.dll >> tmp.def CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o >> chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o >> dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o >> dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o >> sparseQR.o abIndex.o -LD:/erinm/R-3.5.1/bin/x64 -lRlapack >> -LD:/erinm/R-3.5.1/bin/x64 -lRblas -LD:/erinm/R-3.5.1/extsoft/lib/x64 >> -LD:/erinm/R-3.5.1/extsoft/lib -LD:/erinm/R-3.5.1/bin/x64 -lR >> CHMfactor.o:CHMfactor.c:(.text+0x3b): undefined reference to >> `cholmod_copy_factor' >> CHMfactor.o:CHMfactor.c:(.text+0x7b): undefined reference to >> `cholmod_change_factor' >> CHMfactor.o:CHMfactor.c:(.text+0x92): undefined reference to >> `cholmod_factor_to_sparse' >> CHMfactor.o:CHMfactor.c:(.text+0xa5): undefined reference to >> `cholmod_free_factor' >> CHMfactor.o:CHMfactor.c:(.text+0x18e): undefined reference to >> `cholmod_solve' >> CHMfactor.o:CHMfactor.c:(.text+0x267): undefined reference to >> `cholmod_copy_factor' >> CHMfactor.o:CHMfactor.c:(.text+0x27e): undefined reference to >> `cholmod_updown' >> CHMfactor.o:CHMfactor.c:(.text+0x396): undefined reference to >> `cholmod_spsolve' >> CHMfactor.o:CHMfactor.c:(.text+0x620): undefined reference to >> `cholmod_factorize_p' >> CHMfactor.o:CHMfactor.c:(.text+0x658): undefined reference to >> `cholmod_change_factor' >> CHMfactor.o:CHMfactor.c:(.text+0x720): undefined reference to >> `cholmod_copy_factor' >> CHMfactor.o:CHMfactor.c:(.text+0x87b): undefined reference to >> `cholmod_copy_factor' >> CHMfactor.o:CHMfactor.c:(.text+0x8c3): undefined reference to >> `cholmod_free_factor' >> Csparse.o:Csparse.c:(.text+0x9f1): undefined reference to >> `cholmod_sparse_to_dense' >> Csparse.o:Csparse.c:(.text+0xcd6): undefined reference to `cholmod_speye' >> Csparse.o:Csparse.c:(.text+0xd21): undefined reference to `cholmod_add' >> Csparse.o:Csparse.c:(.text+0xd31): undefined reference to >> `cholmod_free_sparse' >> Csparse.o:Csparse.c:(.text+0xd3d): undefined reference to >> `cholmod_copy_sparse' >> Csparse.o:Csparse.c:(.text+0xd4c): undefined reference to >> `cholmod_free_sparse' >> Csparse.o:Csparse.c:(.text+0xdf9): undefined reference to `cholmod_copy' >> >> Does this look familiar, please? >> >> Thanks, >> Erin >> >> Erin Hodgess, PhD >> mailto: erinm.hodg...@gmail.com >> >> >> On Fri, Sep 14, 2018 at 1:13 PM Avraham Adler >> wrote: >> >>> Try following the directions here. They have worked for me for years. >>> Please see the comments too. >>> >>> https://www.avrahamadler.com/r-tips/build-openblas-for-windows-r64/ >>> >>> Hope that helps, >>> >>> Avi >>> >>> On Fri, Sep 14, 2018 at 2:34 PM Erin Hodgess >>> wrote: >>> Hello! I'm building a package that needs Openblas for matrix manipulation speed up. I built Openblas on Windows 10. I updated the MkRules.local, src/extra/blas/Makefile.win, etc. Things are working with "make all". However, when I run "make recommended", I have trouble with the Matrix package build. The components of the Cholesky all appear as unreferenced. Has anyone else run into this, please? I'm working with R-3.5.1 source. Thanks, Erin Erin Hodgess, PhD mailto: erinm.hodg...@gmail.com [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel >>> -- >>> Sent from Gmail Mobile >>> >> -- > 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] Trying to compile R-3.5.1 with openblas for windows
I have a snag on regular BLAS as well. I feel better about the Open BLAS On Fri, Sep 14, 2018 at 2:47 PM Erin Hodgess wrote: > That is my next thing to try. Thanks for your help! > > > Erin Hodgess, PhD > mailto: erinm.hodg...@gmail.com > > > On Fri, Sep 14, 2018 at 2:46 PM Avraham Adler > wrote: > >> No, I’m sorry, I haven’t seen that and I built R 3.5.1 with OpenBLAS >> recently. Does it work if you use the vanilla BLAS? >> >> Avi >> >> On Fri, Sep 14, 2018 at 4:14 PM Erin Hodgess >> wrote: >> >>> Hi again! >>> >>> I checked everything, did "make distribution" and the same thing >>> occurred. >>> >>> >>> d:/Rtools/mingw_64/bin/ar -rucs ../SuiteSparse_config.a >>> SuiteSparse_config.o >>> D:\Rtools\mingw_64\bin\nm.exe: 'sublibs': No such file >>> d:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Matrix.dll >>> tmp.def CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o >>> chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o >>> dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o >>> dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o >>> sparseQR.o abIndex.o -LD:/erinm/R-3.5.1/bin/x64 -lRlapack >>> -LD:/erinm/R-3.5.1/bin/x64 -lRblas -LD:/erinm/R-3.5.1/extsoft/lib/x64 >>> -LD:/erinm/R-3.5.1/extsoft/lib -LD:/erinm/R-3.5.1/bin/x64 -lR >>> CHMfactor.o:CHMfactor.c:(.text+0x3b): undefined reference to >>> `cholmod_copy_factor' >>> CHMfactor.o:CHMfactor.c:(.text+0x7b): undefined reference to >>> `cholmod_change_factor' >>> CHMfactor.o:CHMfactor.c:(.text+0x92): undefined reference to >>> `cholmod_factor_to_sparse' >>> CHMfactor.o:CHMfactor.c:(.text+0xa5): undefined reference to >>> `cholmod_free_factor' >>> CHMfactor.o:CHMfactor.c:(.text+0x18e): undefined reference to >>> `cholmod_solve' >>> CHMfactor.o:CHMfactor.c:(.text+0x267): undefined reference to >>> `cholmod_copy_factor' >>> CHMfactor.o:CHMfactor.c:(.text+0x27e): undefined reference to >>> `cholmod_updown' >>> CHMfactor.o:CHMfactor.c:(.text+0x396): undefined reference to >>> `cholmod_spsolve' >>> CHMfactor.o:CHMfactor.c:(.text+0x620): undefined reference to >>> `cholmod_factorize_p' >>> CHMfactor.o:CHMfactor.c:(.text+0x658): undefined reference to >>> `cholmod_change_factor' >>> CHMfactor.o:CHMfactor.c:(.text+0x720): undefined reference to >>> `cholmod_copy_factor' >>> CHMfactor.o:CHMfactor.c:(.text+0x87b): undefined reference to >>> `cholmod_copy_factor' >>> CHMfactor.o:CHMfactor.c:(.text+0x8c3): undefined reference to >>> `cholmod_free_factor' >>> Csparse.o:Csparse.c:(.text+0x9f1): undefined reference to >>> `cholmod_sparse_to_dense' >>> Csparse.o:Csparse.c:(.text+0xcd6): undefined reference to `cholmod_speye' >>> Csparse.o:Csparse.c:(.text+0xd21): undefined reference to `cholmod_add' >>> Csparse.o:Csparse.c:(.text+0xd31): undefined reference to >>> `cholmod_free_sparse' >>> Csparse.o:Csparse.c:(.text+0xd3d): undefined reference to >>> `cholmod_copy_sparse' >>> Csparse.o:Csparse.c:(.text+0xd4c): undefined reference to >>> `cholmod_free_sparse' >>> Csparse.o:Csparse.c:(.text+0xdf9): undefined reference to `cholmod_copy' >>> >>> Does this look familiar, please? >>> >>> Thanks, >>> Erin >>> >>> Erin Hodgess, PhD >>> mailto: erinm.hodg...@gmail.com >>> >>> >>> On Fri, Sep 14, 2018 at 1:13 PM Avraham Adler >>> wrote: >>> Try following the directions here. They have worked for me for years. Please see the comments too. https://www.avrahamadler.com/r-tips/build-openblas-for-windows-r64/ Hope that helps, Avi On Fri, Sep 14, 2018 at 2:34 PM Erin Hodgess wrote: > Hello! > > I'm building a package that needs Openblas for matrix manipulation > speed up. > > I built Openblas on Windows 10. I updated the MkRules.local, > src/extra/blas/Makefile.win, etc. Things are working with "make all". > > However, when I run "make recommended", I have trouble with the Matrix > package build. The components of the Cholesky all appear as > unreferenced. > > Has anyone else run into this, please? I'm working with R-3.5.1 > source. > > Thanks, > Erin > > Erin Hodgess, PhD > mailto: erinm.hodg...@gmail.com > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > -- Sent from Gmail Mobile >>> -- >> Sent from Gmail Mobile >> > -- Erin Hodgess, PhD mailto: erinm.hodg...@gmail.com [[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] stringi update
Thnaks for the hint, but I have tried several mirrors and still get the same trouble: > update.packages(ask='graphics',checkBuilt=TRUE) There are binary versions available but the source versions are later: binary source needs_compilation stringi 1.1.7 1.2.4 TRUE Do you want to install from sources the packages which need compilation? y/n: Which re-install the same version at each update... Le 10/09/2018 à 17:17, R. Mark Sharp a écrit : Patrick, It looks like the CRAN mirror that you are using has not been updated with the binary versions, which are readily available on other mirrors (e.g., https://cran.revolutionanalytics.com). Mark R. Mark Sharp, Ph.D. Data Scientist and Biomedical Statistical Consultant 7526 Meadow Green St. San Antonio, TX 78251 mobile: 210-218-2868 rmsh...@me.com On Sep 10, 2018, at 12:23 AM, Patrick Giraudoux wrote: Since weeks the package stringi stays on the following versions: update.packages(ask='graphics',checkBuilt=TRUE) There is a binary version available but the source version is later: binary source needs_compilation stringi 1.1.7 1.2.4 TRUE Do you want to install from sources the package which needs compilation? y/n: n However updated, I am asked to update it again with the same version at any next update of R. Has somebody an idea about what is happening? Patrick __ 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
