On 21 June 2018 at 09:59, Yifang Tan wrote: | 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!
Awesome!! | 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. RStudio knows what they are doing; their version will not spill. Anaconda I am less sure -- my general recommendation is to keep Anaconda away and out of your path. At a minimum you can build in a more restrictive environment (say a Docker container, or a chroot as Debian does) to avoid the spills. Dirk | | Best, | | Yifang | | On Wed, Jun 20, 2018 at 4:35 PM, Dirk Eddelbuettel <e...@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@r-project.org | > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian | > | > -- | > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | > -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian