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

[Yifang Tan]

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

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