[R-sig-Debian] libR.so error to install R-3.5.0 in Ubuntu 18.04

[Dirk Eddelbuettel]

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 <edd using 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 using r-project.org
| > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| >
| > --
| > http://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
| >

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org