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R language seemingly broken in latest version and having major problems with plotting package

  • 1.  R language seemingly broken in latest version and having major problems with plotting package

    Posted Thu December 15, 2022 01:56 PM
    R language seemingly broken in latest version and having major problems with plotting package

    Working with a client, we installed the latest version of R-4.1.2. Then we had trouble installing packages within R. We couldn't get ggplot2 working and others as well.
    So after troubleshooting, I noticed under R>capabilities() the following showed:


    We then tried to build/configure R-4.1.2 from the official cran r project source. During configure we installed a number of the latest devel rpms from AIX toolbox and was able to build R-4.1.2. Then we took the SRPM from AIX toolbox and built the RPM for R-4.1.2.
    Then we reinstalled R, and saw that jpeg, png, tiff, and cairo had support.

    WE then proceed to reinstall ggplot2 successfully. When we go to run our application, ggplot2 commands will not run. It aborts every time we try to run anything under.

    I thought this might be an isolated case, but we now have several customers with this problem.

    $ oslevel -s
    7200-03-07-2114

    Here is the current customers RPM's :
    $ rpm -qa
    expect-5.42.1-3.ppc
    vim-common-6.3-1.ppc
    osinstall-1.6-1.noarch
    less-382-1.ppc
    vim-enhanced-6.3-1.ppc
    teagent-realtime-0.9-1.ppc
    python-2.7.10-1.ppc
    python-iniparse-0.4-1.noarch
    python-urlgrabber-3.10.1-1.noarch
    python-devel-2.7.10-1.ppc
    libgcc8-8.3.0-6.ppc
    libstdc++8-8.3.0-6.ppc
    libstdc++-8-1.ppc
    libgomp8-8.3.0-6.ppc
    xz-libs-5.2.5-1.ppc
    libtextstyle-0.21-2.ppc
    libunistring-0.9.10-1.ppc
    bash-5.1.16-1.ppc
    expat-2.4.9-1.ppc
    libcomps-devel-0.1.11-101.ppc
    gdbm-1.23-1.ppc
    sqlite-3.39.3-1.ppc
    gmp-6.2.1-1.ppc
    libmpc-1.2.1-1.ppc
    freetype2-2.12.1-1.ppc
    libXrender-0.9.8-3waixX11.ppc
    sed-4.8-1.ppc
    gcc8-cpp-8.3.0-6.ppc
    gcc-8-1.ppc
    gcc-gfortran-8-1.ppc
    harfbuzz-5.2.0-1.ppc
    libwebp-1.0.2-1.ppc
    cyrus-sasl-2.1.28-1.ppc
    pcre-8.44-2.ppc
    libgfortran-8-1.ppc
    libstdc++8-devel-8.3.0-6.ppc
    gcc-c++-8-1.ppc
    gettext-0.21-2.ppc
    freetype2-devel-2.12.1-1.ppc
    glib2-devel-2.56.1-3.ppc
    fontconfig-devel-2.11.95-4.ppc
    libXrender-devel-0.9.8-3waixX11.ppc
    apr-1.7.0-1.ppc
    httpd-2.4.54-3.ppc
    xz-devel-5.2.5-1.ppc
    libssh2-devel-1.10.0-1.ppc
    pkg-config-0.29.2-2.ppc
    cairo-1.14.6-2waixX11.ppc
    libtiff-4.4.0-1.ppc
    jbigkit-devel-2.1-1.ppc
    libjpeg-devel-9e-1.ppc
    readline-devel-8.1-1.ppc
    openldap-devel-2.4.58-4.ppc
    texinfo-6.7-1.ppc
    pcre-devel-8.44-2.ppc
    libtasn1-4.16.0-1.ppc
    p11-kit-tools-0.23.22-1.ppc
    krb5-libs-1.18.5-2.ppc
    curl-7.85.0-1.ppc
    R-devel-4.1.2-1.ppc
    tcl-8.4.7-3.ppc
    wget-1.9.1-1.ppc
    tk-8.4.7-3.ppc
    MFEcma-4.8.0-1938.ppc
    TWeagent-8.7.3.4-0.ppc
    yum-metadata-parser-1.1.4-2.ppc
    pysqlite-1.1.7-2.ppc
    python-pycurl-7.19.3-1.ppc
    yum-3.4.3-8.noarch
    python-tools-2.7.10-1.ppc
    AIX-rpm-7.2.5.103-19.ppc
    libgcc-8-1.ppc
    zlib-1.2.12-1.ppc
    ncurses-6.3-1.ppc
    libgomp-8-1.ppc
    libffi-3.4.2-1.ppc
    glib2-2.56.1-3.ppc
    libxml2-2.10.2-1.ppc
    libiconv-1.17-1.ppc
    info-6.7-1.ppc
    libcomps-0.1.11-101.ppc
    bzip2-1.0.8-2.ppc
    readline-8.1-1.ppc
    python3-3.7.12-1.ppc
    mpfr-4.1.0-1.ppc
    libpng-1.6.37-1.ppc
    fontconfig-2.11.95-4.ppc
    libgfortran8-8.3.0-6.ppc
    gcc8-8.3.0-6.ppc
    pixman-0.34.0-1.ppc
    gcc-cpp-8-1.ppc
    gcc8-gfortran-8.3.0-6.ppc
    libXft-2.3.2-4waixX11.ppc
    libssh2-1.10.0-1.ppc
    db-5.3.28-1.ppc
    openldap-2.4.58-4.ppc
    pcre2-10.40-1.ppc
    jbigkit-libs-2.1-1.ppc
    lzo-2.10-2.ppc
    pango-1.40.1-2waixX11.ppc
    gcc8-c++-8.3.0-6.ppc
    unzip-6.0-3.ppc
    gettext-devel-0.21-2.ppc
    zlib-devel-1.2.12-1.ppc
    libpng-devel-1.6.37-1.ppc
    expat-devel-2.4.9-1.ppc
    renderproto-0.11.1-1.ppc
    apr-util-1.6.1-1.ppc
    bzip2-devel-1.0.8-2.ppc
    pcre2-devel-10.40-1.ppc
    aix-x11-pc-1.0-1.ppc
    libjpeg-9e-1.ppc
    cairo-devel-1.14.6-2waixX11.ppc
    libtiff-devel-4.4.0-1.ppc
    pixman-devel-0.34.0-1.ppc
    bison-3.8.2-2.ppc
    perl-5.34.1-1.ppc
    xproto-devel-7.0.28-3.ppc
    make-4.3-1.ppc
    curl-devel-7.85.0-1.ppc
    p11-kit-0.23.22-1.ppc
    ca-certificates-2021.2.52-3.ppc
    libnghttp2-1.46.0-1.ppc
    R-4.1.2-1.ppc

    ------------------------------
    VINCE DAVIS
    ------------------------------

    #AIXOpenSource


  • 2.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Thu December 15, 2022 10:49 PM
    Hi
    i have seen on R Cran page taht R 4.2.2 is out...maybe we should install this level and mybe the problem is solved ?

    ------------------------------
    Vincencio Michaelis
    ------------------------------

    Original Message


  • 3.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Thu December 15, 2022 11:24 PM
    Hi
    i have downloaded latest R 4.2.2 and tried to install but got error message when doing

    root@rb3zf01(Si):/cpt/vince/R-4.2.2 $ ./configure --with-readline=no --with-x=no


    .........

    checking for ndir.h that defines DIR... no
    checking for library containing opendir... no
    configure: error: Building R requires the 'opendir' system call
     


    ------------------------------
    Vincencio Michaelis
    ------------------------------

    Original Message


  • 4.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Mon December 19, 2022 12:13 PM
    Vince try to install pkg-config

    ------------------------------
    VINCE DAVIS
    ------------------------------

    Original Message


  • 5.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Fri December 16, 2022 05:19 AM
    The 4.1.2 build in Toolbox was missing some capabilities. We will fix and update Toolbox with a new R release 4.1.2-2.
    The issue is not because of the R version itself because I am able to rebuild and test with ggplot2
    As far as your local build is concerned, I am not sure why ggplot2 is aborting.

    ------------------------------
    Ayappan P
    ------------------------------

    Original Message


  • 6.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Mon December 19, 2022 06:54 AM
    hi
    when do you think is 4.12-2 available ?
    thx
    vince

    ------------------------------
    Vincencio Michaelis
    ------------------------------

    Original Message


  • 7.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Mon December 19, 2022 08:26 AM
    We are working on it. There are couple of issues reported by another user as well. 
    Probably if everything goes smooth, it will be available end of this week (Friday).

    ------------------------------
    Ayappan P
    ------------------------------

    Original Message


  • 8.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Fri December 23, 2022 09:12 AM
    R-4.1.2-2 is now available in AIX Toolbox.

    ------------------------------
    Ayappan P
    ------------------------------

    Original Message


  • 9.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Wed January 04, 2023 02:20 AM
    Hi
    i have updated to 4.1.2-2 but got error now in IBM CPT Programm:

    Error in ggplot() : could not find function "ggplot"
    Calls: entplot
    Execution halted



    root@rb3zf01(Si):/cpt/logs $ rpm -qa|grep R
    R-devel-4.1.2-2.ppc
    R-4.1.2-2.ppc




    ------------------------------
    Vincencio Michaelis
    ------------------------------

    Original Message


  • 10.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Mon January 09, 2023 08:56 AM
    Can you try reinstalling ggplot2 through R and verify ggplot by doing some sample plots after exporting DISPLAY.

    install.packages("ggplot2")
    library("ggplot2")
    ggplot(iris, aes(x=Sepal.Length, y=Petal.Length, col=Species))+geom_point() 

    ------------------------------
    Ayappan P
    ------------------------------

    Original Message


  • 11.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Mon January 09, 2023 09:31 AM
    Hi
    can you please provide all commands needed in detail ? I dont know anything about R ,ggplot etc.
    thx
    vince

    ------------------------------
    Vincencio Michaelis
    ------------------------------

    Original Message


  • 12.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Mon January 09, 2023 12:33 PM

    # export STRINGI_DISABLE_CXX11=yes

        # export with_extra_ldflags="-Wl,-bbigtoc"

           # /opt/freeware/bin/R

        ...

        > install.packages("ggplot2", repos="http://cran.r-project.org")

        > install.packages("data.table", repos="http://cran.r-project.org")



    ------------------------------
    VINCE DAVIS
    ------------------------------

    Original Message


  • 13.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Mon January 09, 2023 11:30 PM
    Hi Vince
    thx for the update...my problem is i have no internet access from thix AIX except DNF to IBM......so i need things offline to download and the load into AIX R config
     
    root@rb3zf01(Si):/tmp $ export STRINGI DISABLE CXX11=yes
    root@rb3zf01(Si):/tmp $ export with extra ldflags="-Wl,-bbigtoc"
    root@rb3zf01(Si):/tmp $ /opt/freeware/bin/R

    R version 4.1.2 (2021-11-01) -- "Bird Hippie"
    Copyright (C) 2021 The R Foundation for Statistical Computing
    Platform: powerpc-ibm-aix7.1.3.0 (64-bit)

    R is free software and comes with ABSOLUTELY NO WARRANTY.
    You are welcome to redistribute it under certain conditions.
    Type 'license()' or 'licence()' for distribution details.

    Natural language support but running in an English locale

    R is a collaborative project with many contributors.
    Type 'contributors()' for more information and
    'citation()' on how to cite R or R packages in publications.

    Type 'demo()' for some demos, 'help()' for on-line help, or
    'help.start()' for an HTML browser interface to help.
    Type 'q()' to quit R.

    ^[[?2004h> ^[[7minstall.packages("ggplot2", repos="http://cran.r-project.org")^[[m^M> install.packages("ggplot2", repos="http://cran.r-project.org")
    ^[[?2004l^MWarning: unable to access index for repository http://cran.r-project.org/src/contrib:
    cannot open URL 'http://cran.r-project.org/src/contrib/PACKAGES'
    Warning message:
    package 'ggplot2' is not available for this version of R

    A version of this package for your version of R might be available elsewhere,
    see the ideas at
    https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
    ^[[?2004h> ^[[7minstall.packages("data.table", repos="http://cran.r-project.org")^[[m^M> install.packages("data.table", repos="http://cran.r-project.org")
    ^[[?2004l^MWarning: unable to access index for repository http://cran.r-project.org/src/contrib:
    cannot open URL 'http://cran.r-project.org/src/contrib/PACKAGES'
    Warning message:
    package 'data.table' is not available for this version of R

    A version of this package for your version of R might be available elsewhere,
    see the ideas at
    https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

    ------------------------------
    Vincencio Michaelis
    ------------------------------

    Original Message


  • 14.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Tue January 10, 2023 12:15 AM
    Hi
    i have downloaded ggplot2 manually from project download page because this http site is not allowed internally from bosch to access from any AIX system.
    when builidng ggplot2 i got:


    root@rb3zf01(Si):/cpt/Rpackages $ R CMD build ggplot2
    * checking for file 'ggplot2/DESCRIPTION' ... OK
    * preparing 'ggplot2':
    * checking DESCRIPTION meta-information ... OK
    Error in loadVignetteBuilder(pkgdir, TRUE) :
    vignette builder 'knitr' not found
    Execution halted
    rm: 0653-610 Cannot remove current directory /tmp/RtmpAAlqia/Rbuild2d029a2f925221.


    so i have downloaded knitr and try to build this:

    root@rb3zf01(Si):/cpt/Rpackages $ R CMD build knitr
    root@rb3zf01(Si):/cpt/Rpackages $ ls -ltr knitr
    total 112
    -rw-r--r-- 1 1010 usr 34 Nov 03 2013 .Rinstignore
    drwxr-xr-x 2 1010 usr 256 Oct 11 2018 demo
    -rw-r--r-- 1 1010 usr 3687 Jul 21 17:30 NAMESPACE
    drwxr-xr-x 2 1010 usr 4096 Aug 09 22:26 man
    drwxr-xr-x 3 1010 usr 256 Nov 10 00:23 tests
    drwxr-xr-x 2 1010 usr 4096 Nov 10 18:40 R
    drwxr-xr-x 9 1010 usr 4096 Nov 17 00:30 inst
    drwxr-xr-x 2 1010 usr 256 Nov 17 00:30 build
    drwxr-xr-x 3 1010 usr 4096 Nov 17 00:30 vignettes
    -rw-r--r-- 1 1010 usr 18596 Nov 18 13:00 MD5
    -rw-r--r-- 1 1010 usr 10194 Nov 18 13:00 DESCRIPTION
    root@rb3zf01(Si):/cpt/Rpackages $ R CMD build knitr
    * checking for file 'knitr/DESCRIPTION' ... OK
    * preparing 'knitr':
    * checking DESCRIPTION meta-information ... OK
    Error in loadVignetteBuilder(pkgdir, TRUE) :
    vignette builder 'knitr' not found
    Execution halted
    rm: 0653-610 Cannot remove current directory /tmp/RtmpiQRMia/Rbuildd7024465283a1.



    this drives me crazy....why is IBM not able to setup everything and send to customer only the needed R directories please ?
    thx
    vince




    ------------------------------
    Vincencio Michaelis
    ------------------------------

    Original Message


  • 15.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Tue January 10, 2023 01:02 AM
    "R CMD build" will create just a package source tarball ,useless in your case. ( You can skip this error by passing "--no-build-vignettes" ).
    What you need is "R CMD INSTALL ggplot2". BTW, ggplot2 has many dependencies [ 'cli', 'glue', 'gtable', 'isoband', 'lifecycle', 'rlang', 'scales', 'tibble', 'vctrs', 'withr' ].
    Without an internet access , probably you need to download all these manually and install it. 
    You can probably look into this GitHub project which helps this particular scenario --> https://github.com/dewittpe/R-install-dependencies

    ------------------------------
    Ayappan P
    ------------------------------

    Original Message


  • 16.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Tue January 10, 2023 01:12 AM
    Hi
    that was the reason why i have asked IBM to deliver R ready to use as we got it from CPT Install when did install very first time.....
    now i got other errors...


    root@rb3zf01(Si):/cpt/Rpackages $ R CMD INSTALL ggplot2 --no-build-vignettes
    Warning: unknown option '--no-build-vignettes'
    * installing to library '/opt/freeware/lib64/R/library'
    * installing *source* package 'ggplot2' ...
    ** package 'ggplot2' successfully unpacked and MD5 sums checked
    ** using staged installation
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in dyn.load(file, DLLpath = DLLpath, ...) :
    unable to load shared object '/opt/freeware/lib64/R/library/rlang/libs/rlang.so':
    rtld: 0712-001 Symbol finite was referenced
    from module /opt/freeware/lib64/R/library/rlang/libs/rlang.so(), but a runtime definition
    of the symbol was not found.
    rtld: 0712-001 Symbol strcmp was referenced
    from module /opt/freeware/lib64/R/library/rlang/libs/rlang.so(), but a runtime definition
    of the symbol was not found.
    rtld: 0712-001 Symbol memcpy was referenced
    from module /opt/freeware/lib64/R/library/rlang/libs/rlang.so(), but a runtime definition
    of the symbol was not found.
    rtld: 0712-001 Symbol floor was referenced
    from module /opt/freeware/lib64/R/library/rlang/libs/rlang.so(), but a runtime definition
    of the symbol was not found.
    Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
    Execution halted
    ERROR: lazy loading failed for package 'ggplot2'
    * removing '/opt/freeware/lib64/R/library/ggplot2'
    * restoring previous '/opt/freeware/lib64/R/library/ggplot2'
    root@rb3zf01(Si):/cpt/Rpackages $

    ------------------------------
    Vincencio Michaelis
    ------------------------------

    Original Message


  • 17.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Tue January 10, 2023 01:36 AM

    R-4.1.2-2 has a fix which removes duplicate symbols from R library. 

    https://community.ibm.com/community/user/power/discussion/problems-with-r-libiconv-and-gcc?ReturnUrl=%2fcommunity%2fuser%2fpower%2fcommunities%2fcommunity-home%2fdigestviewer%3fcommunitykey%3d10c1d831-47ee-4d92-a138-b03f7896f7c9

    So you need to remove the already installed modules (modules installed using R-4.1.2-1 ) and install it again. 



    ------------------------------
    Ayappan P
    ------------------------------

    Original Message


  • 18.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Tue January 10, 2023 02:26 AM
    i was able now to recompile ggplot2 and i will do a new run for IBM CPT and see what happens...thx vince

    ------------------------------
    Vincencio Michaelis
    ------------------------------

    Original Message


  • 19.  RE: R language seemingly broken in latest version and having major problems with plotting package

    Posted Wed January 04, 2023 02:20 AM
    root@rb3zf01(Si):/cpt/logs $ rpm -qa
    netcat-1.10-3.ppc
    cairo-1.14.6-2waixX11.ppc
    patch-2.7.6-1.ppc
    b315191014103506-001600231021-1.noarch
    fontconfig-2.11.95-4.ppc
    lzo-2.10-2.ppc
    lsof-4.89-1.ppc
    libXft-2.3.2-4waixX11.ppc
    sudo-1.9.5p2-1.ppc
    pcre-8.44-2.ppc
    libgcc-8-1.ppc
    libstdc++-8-1.ppc
    libgomp8-8.3.0-6.ppc
    libstdc++8-devel-8.3.0-6.ppc
    tcl-8.6.11-1.ppc
    libgfortran-8-1.ppc
    libXrender-0.9.8-3waixX11.ppc
    glib2-2.56.1-3.ppc
    readline-8.1-1.ppc
    gcc8-cpp-8.3.0-6.ppc
    gcc8-c++-8.3.0-6.ppc
    gcc-cpp-8-1.ppc
    p11-kit-0.23.22-1.ppc
    gcc-c++-8-1.ppc
    cpio-2.13-1.ppc
    popt-1.18-1.ppc
    tk-8.6.11-1.ppc
    lua-5.4.1-1.ppc
    libconfuse-3.2.2-2.ppc
    b315191014103506-001600311014-1.noarch
    xz-libs-5.2.5-1.ppc
    gdbm-1.23-1.ppc
    python3.9-3.9.6-1.ppc
    python3.9-idle-3.9.6-1.ppc
    python3.9-test-3.9.6-1.ppc
    AIX-rpm-7.2.5.101-33.ppc
    zlib-1.2.12-1.ppc
    libxml2-2.9.14-1.ppc
    expat-2.4.6-1.ppc
    gmp-6.2.1-1.ppc
    libsmartcols-2.34-100.ppc
    check-0.13.0-1.ppc
    libpng-1.6.37-1.ppc
    libyaml-0.2.5-1.ppc
    apr-1.7.0-1.ppc
    libksba-1.6.0-1.ppc
    nettle-3.7.3-1.ppc
    mpfr-4.1.0-1.ppc
    file-libs-5.41-1.ppc
    nspr-4.32-1.ppc
    python3-3.7.12-1.ppc
    krb5-libs-1.18.5-1.ppc
    openldap-2.4.58-3.ppc
    httpd-2.4.54-1.ppc
    pcre2-10.40-1.ppc
    libwebp-1.0.2-1.ppc
    curl-7.83.1-1.ppc
    libsolv-0.7.9-32_51.ppc
    gpgme-1.13.1-100.ppc
    libdnf-0.39.1-32_50.ppc
    python3-hawkey-0.39.1-32_50.ppc
    python3-dnf-4.2.17-32_50.ppc
    jbigkit-libs-2.1-1.ppc
    dnf-automatic-4.2.17-32_50.ppc
    mod_ssl-2.4.54-1.ppc
    file-5.41-1.ppc
    harfbuzz-4.3.0-1.ppc
    vim-common-8.2.5172-1.ppc
    less-598-1.ppc
    ruby-2.7.5-1.ppc
    gettext-0.21-2.ppc
    wget-1.21.2-1.ppc
    freetype2-devel-2.12.1-1.ppc
    renderproto-0.11.1-1.ppc
    python-2.7.18-3.ppc
    expat-devel-2.4.6-1.ppc
    cairo-devel-1.14.6-2waixX11.ppc
    R-devel-4.1.2-2.ppc
    rsync_64-3.1.1-1.ppc
    deltarpm-3.6-1.ppc
    pixman-0.34.0-1.ppc
    unzip-64bit-6.0-5.ppc
    bzip2-1.0.8-2.ppc
    libidn-1.33-1.ppc
    libgcc8-8.3.0-6.ppc
    libstdc++8-8.3.0-6.ppc
    db-5.3.28-1.ppc
    libgomp-8-1.ppc
    libtasn1-4.16.0-1.ppc
    libgfortran8-8.3.0-6.ppc
    libjpeg-9d-1.ppc
    bash-5.1.4-2.ppc
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    root@rb3zf01(Si):/cpt/logs $

    ------------------------------
    Vincencio Michaelis
    ------------------------------

    Original Message


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