Yifang Tan
2018-Jun-20 22:12 UTC
[R-sig-Debian] libR.so error to install R-3.5.0 in Ubuntu 18.04
I tried to install R-3.5.0 from source on my Ubuntu 18.04, and met this problem: ../../lib/libR.so: undefined reference to 'ucol_strcollIter_58' ../../lib/libR.so: undefined reference to 'u_getVersion_58' ../../lib/libR.so: undefined reference to 'uloc_setDefault_58' ../../lib/libR.so: undefined reference to 'ucol_close_58' ../../lib/libR.so: undefined reference to 'ucol_getLocaleByType_58' ../../lib/libR.so: undefined reference to 'ucol_setAttribute_58' ../../lib/libR.so: undefined reference to 'u_versionToString_58' ../../lib/libR.so: undefined reference to 'ucol_open_58' ../../lib/libR.so: undefined reference to 'uiter_setUTF8_58' ../../lib/libR.so: undefined reference to 'ucol_setStrength_58' # collect2: error: ld returned 1 exit status # Makefile:145: recipe for target 'R.bin' failed What I did to configure is according to the INSTALL instruction with the source code except --with-cairo (which seems un-necessary): ./configure --prefix=/opt/R/3.5.0 --enable-R-shlib --with-blas --with-lapack --with-cairo ################################################################################### # R is now configured for x86_64-pc-linux-gnu # # Source directory: . # Installation directory: /opt/R/3.5.0 # # C compiler: gcc -g -O2 # Fortran 77 compiler: f95 -g -O2 # # Default C++ compiler: g++ -g -O2 # C++98 compiler: g++ -std=gnu++98 -g -O2 # C++11 compiler: g++ -std=gnu++11 -g -O2 # C++14 compiler: g++ -std=gnu++14 -g -O2 # C++17 compiler: g++ -std=gnu++17 -g -O2 # Fortran 90/95 compiler: gfortran -g -O2 # Obj-C compiler: # # Interfaces supported: X11, tcltk # External libraries: readline, BLAS(generic), LAPACK(generic), curl # Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU # Options enabled: shared R library, R profiling # # Capabilities skipped: # Options not enabled: shared BLAS, memory profiling # # Recommended packages: yes # ################################################################################################## The above error came from make by sudo make. There are some threads about the options --enable-R-shlib, but the problem stayed with the option turned off. Without --with-cairo option could not resolve the problem either. After several hours of search, it seems to me it is related to the compiling process, but I'm not sure which library is missing, or which options should be used to compile/link in my Ubuntu 18.04. Thanks a lot! Yifang [[alternative HTML version deleted]]
Ista Zahn
2018-Jun-20 22:30 UTC
[R-sig-Debian] libR.so error to install R-3.5.0 in Ubuntu 18.04
You can make sure you have all packages required to build with apt-get build-dep r-base Note that you shouldn't use sudo to make, just the usual ./configure make sudo make install Best, Ista On Wed, Jun 20, 2018 at 6:12 PM, Yifang Tan <yifangt at gmail.com> wrote:> I tried to install R-3.5.0 from source on my Ubuntu 18.04, and met this > problem: > > ../../lib/libR.so: undefined reference to 'ucol_strcollIter_58' > ../../lib/libR.so: undefined reference to 'u_getVersion_58' > ../../lib/libR.so: undefined reference to 'uloc_setDefault_58' > ../../lib/libR.so: undefined reference to 'ucol_close_58' > ../../lib/libR.so: undefined reference to 'ucol_getLocaleByType_58' > ../../lib/libR.so: undefined reference to 'ucol_setAttribute_58' > ../../lib/libR.so: undefined reference to 'u_versionToString_58' > ../../lib/libR.so: undefined reference to 'ucol_open_58' > ../../lib/libR.so: undefined reference to 'uiter_setUTF8_58' > ../../lib/libR.so: undefined reference to 'ucol_setStrength_58' > > # collect2: error: ld returned 1 exit status > # Makefile:145: recipe for target 'R.bin' failed > > What I did to configure is according to the INSTALL instruction with the > source code except --with-cairo (which seems un-necessary): > > ./configure --prefix=/opt/R/3.5.0 --enable-R-shlib --with-blas > --with-lapack --with-cairo > > ################################################################################### > # R is now configured for x86_64-pc-linux-gnu > # > # Source directory: . > # Installation directory: /opt/R/3.5.0 > # > # C compiler: gcc -g -O2 > # Fortran 77 compiler: f95 -g -O2 > # > # Default C++ compiler: g++ -g -O2 > # C++98 compiler: g++ -std=gnu++98 -g -O2 > # C++11 compiler: g++ -std=gnu++11 -g -O2 > # C++14 compiler: g++ -std=gnu++14 -g -O2 > # C++17 compiler: g++ -std=gnu++17 -g -O2 > # Fortran 90/95 compiler: gfortran -g -O2 > # Obj-C compiler: > # > # Interfaces supported: X11, tcltk > # External libraries: readline, BLAS(generic), LAPACK(generic), > curl > # Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU > # Options enabled: shared R library, R profiling > # > # Capabilities skipped: > # Options not enabled: shared BLAS, memory profiling > # > # Recommended packages: yes > # > ################################################################################################## > The above error came from make by sudo make. > > There are some threads about the options --enable-R-shlib, but the problem > stayed with the option turned off. Without --with-cairo option could not > resolve the problem either. > After several hours of search, it seems to me it is related to the > compiling process, but I'm not sure which library is missing, or which > options should be used to compile/link in my Ubuntu 18.04. > > Thanks a lot! > > Yifang > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Dirk Eddelbuettel
2018-Jun-20 22:35 UTC
[R-sig-Debian] libR.so error to install R-3.5.0 in Ubuntu 18.04
On 20 June 2018 at 16:12, Yifang Tan wrote: | I tried to install R-3.5.0 from source on my Ubuntu 18.04, Why? The binaries we offer via CRAN are _excellent_. I maintain the underlying Debian source and use them myself on several machines, and have for years. Just read https://cloud.r-project.org/bin/linux/ubuntu/README.html and follow the instructions. Otherwise ... | and met this problem: | | ../../lib/libR.so: undefined reference to 'ucol_strcollIter_58' | ../../lib/libR.so: undefined reference to 'u_getVersion_58' | ../../lib/libR.so: undefined reference to 'uloc_setDefault_58' | ../../lib/libR.so: undefined reference to 'ucol_close_58' | ../../lib/libR.so: undefined reference to 'ucol_getLocaleByType_58' | ../../lib/libR.so: undefined reference to 'ucol_setAttribute_58' | ../../lib/libR.so: undefined reference to 'u_versionToString_58' | ../../lib/libR.so: undefined reference to 'ucol_open_58' | ../../lib/libR.so: undefined reference to 'uiter_setUTF8_58' | ../../lib/libR.so: undefined reference to 'ucol_setStrength_58' | | # collect2: error: ld returned 1 exit status | # Makefile:145: recipe for target 'R.bin' failed You somehow messed something up with libicu* -- looks like you built again version 58 but you don't have it (not sure how). | | What I did to configure is according to the INSTALL instruction with the | source code except --with-cairo (which seems un-necessary): Those are generic instructions so you could ask on r-devel :) Seriously, nothing in the R Inst + Admin manual is specific to Debian or Ubuntu. The rest below looks fine. Your problem is a different one, somehow. But as I said, why not do what I a bazillion other people do and just use the binary? Otherwise, you can see my (Debian) builds files here https://salsa.debian.org/edd/r-base/tree/master/debian/rules https://salsa.debian.org/edd/r-base/tree/master/debian/control and they should carry over easily to 18.04, and with possible adjustments to 16.04, 14.04 and others. I don't think Michael's sources are in git though (hint, hint, ...) Dirk | ./configure --prefix=/opt/R/3.5.0 --enable-R-shlib --with-blas | --with-lapack --with-cairo | | ################################################################################### | # R is now configured for x86_64-pc-linux-gnu | # | # Source directory: . | # Installation directory: /opt/R/3.5.0 | # | # C compiler: gcc -g -O2 | # Fortran 77 compiler: f95 -g -O2 | # | # Default C++ compiler: g++ -g -O2 | # C++98 compiler: g++ -std=gnu++98 -g -O2 | # C++11 compiler: g++ -std=gnu++11 -g -O2 | # C++14 compiler: g++ -std=gnu++14 -g -O2 | # C++17 compiler: g++ -std=gnu++17 -g -O2 | # Fortran 90/95 compiler: gfortran -g -O2 | # Obj-C compiler: | # | # Interfaces supported: X11, tcltk | # External libraries: readline, BLAS(generic), LAPACK(generic), | curl | # Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU | # Options enabled: shared R library, R profiling | # | # Capabilities skipped: | # Options not enabled: shared BLAS, memory profiling | # | # Recommended packages: yes | # | ################################################################################################## | The above error came from make by sudo make. | | There are some threads about the options --enable-R-shlib, but the problem | stayed with the option turned off. Without --with-cairo option could not | resolve the problem either. | After several hours of search, it seems to me it is related to the | compiling process, but I'm not sure which library is missing, or which | options should be used to compile/link in my Ubuntu 18.04. | | Thanks a lot! | | Yifang | | [[alternative HTML version deleted]] | | _______________________________________________ | R-SIG-Debian mailing list | R-SIG-Debian at r-project.org | https://stat.ethz.ch/mailman/listinfo/r-sig-debian -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Yifang Tan
2018-Jun-21 15:59 UTC
[R-sig-Debian] libR.so error to install R-3.5.0 in Ubuntu 18.04
Thanks Dirk! I wrongly thought the R-3.5.0 Binary was NOT default R for Ubuntu 18.04 as some of my R packages requires updated R version. Anyway, with your suggestion all went well like charm. Thank you very much! Back to the problem, actually I saw different versions of libicu* such as: /home/yifang/anaconda3/lib/libicudata.so.58 /home/yifang/anaconda3/pkgs/icu-58.2-h9c2bf20_1/lib/libicuio.so.58 /opt/anaconda3/lib/libicuio.so.58 /opt/anaconda3/pkgs/icu-58.2-h9c2bf20_1/lib/libicudata.so.58 /usr/lib/rstudio/bin/libicudata.so.55 /usr/lib/x86_64-linux-gnu/libicudata.so.60 /usr/share/doc/libiculx60 /var/lib/dpkg/info/libicu60:amd64.shlibs I had thought the anaconda3 library (version 58) and rstudio (using version 55) conflict with shared libicu* version 60, exactly as you pointed out. How to resolve my problem for educational purpose? Appreciate your insights. Best, Yifang On Wed, Jun 20, 2018 at 4:35 PM, Dirk Eddelbuettel <edd at debian.org> wrote:> > On 20 June 2018 at 16:12, Yifang Tan wrote: > | I tried to install R-3.5.0 from source on my Ubuntu 18.04, > > Why? > > The binaries we offer via CRAN are _excellent_. I maintain the underlying > Debian source and use them myself on several machines, and have for years. > > Just read https://cloud.r-project.org/bin/linux/ubuntu/README.html > and > follow the instructions. > > Otherwise ... > > | and met this problem: > | > | ../../lib/libR.so: undefined reference to 'ucol_strcollIter_58' > | ../../lib/libR.so: undefined reference to 'u_getVersion_58' > | ../../lib/libR.so: undefined reference to 'uloc_setDefault_58' > | ../../lib/libR.so: undefined reference to 'ucol_close_58' > | ../../lib/libR.so: undefined reference to 'ucol_getLocaleByType_58' > | ../../lib/libR.so: undefined reference to 'ucol_setAttribute_58' > | ../../lib/libR.so: undefined reference to 'u_versionToString_58' > | ../../lib/libR.so: undefined reference to 'ucol_open_58' > | ../../lib/libR.so: undefined reference to 'uiter_setUTF8_58' > | ../../lib/libR.so: undefined reference to 'ucol_setStrength_58' > | > | # collect2: error: ld returned 1 exit status > | # Makefile:145: recipe for target 'R.bin' failed > > You somehow messed something up with libicu* -- looks like you built again > version 58 but you don't have it (not sure how). > | > | What I did to configure is according to the INSTALL instruction with the > | source code except --with-cairo (which seems un-necessary): > > Those are generic instructions so you could ask on r-devel :) Seriously, > nothing in the R Inst + Admin manual is specific to Debian or Ubuntu. > > The rest below looks fine. Your problem is a different one, somehow. But > as I > said, why not do what I a bazillion other people do and just use the > binary? > > Otherwise, you can see my (Debian) builds files here > > https://salsa.debian.org/edd/r-base/tree/master/debian/rules > https://salsa.debian.org/edd/r-base/tree/master/debian/control > > and they should carry over easily to 18.04, and with possible adjustments > to > 16.04, 14.04 and others. I don't think Michael's sources are in git though > (hint, hint, ...) > > Dirk > > | ./configure --prefix=/opt/R/3.5.0 --enable-R-shlib --with-blas > | --with-lapack --with-cairo > | > | ############################################################ > ####################### > | # R is now configured for x86_64-pc-linux-gnu > | # > | # Source directory: . > | # Installation directory: /opt/R/3.5.0 > | # > | # C compiler: gcc -g -O2 > | # Fortran 77 compiler: f95 -g -O2 > | # > | # Default C++ compiler: g++ -g -O2 > | # C++98 compiler: g++ -std=gnu++98 -g -O2 > | # C++11 compiler: g++ -std=gnu++11 -g -O2 > | # C++14 compiler: g++ -std=gnu++14 -g -O2 > | # C++17 compiler: g++ -std=gnu++17 -g -O2 > | # Fortran 90/95 compiler: gfortran -g -O2 > | # Obj-C compiler: > | # > | # Interfaces supported: X11, tcltk > | # External libraries: readline, BLAS(generic), LAPACK(generic), > | curl > | # Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU > | # Options enabled: shared R library, R profiling > | # > | # Capabilities skipped: > | # Options not enabled: shared BLAS, memory profiling > | # > | # Recommended packages: yes > | # > | ############################################################ > ###################################### > | The above error came from make by sudo make. > | > | There are some threads about the options --enable-R-shlib, but the > problem > | stayed with the option turned off. Without --with-cairo option could not > | resolve the problem either. > | After several hours of search, it seems to me it is related to the > | compiling process, but I'm not sure which library is missing, or which > | options should be used to compile/link in my Ubuntu 18.04. > | > | Thanks a lot! > | > | Yifang > | > | [[alternative HTML version deleted]] > | > | _______________________________________________ > | R-SIG-Debian mailing list > | R-SIG-Debian at r-project.org > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org >[[alternative HTML version deleted]]