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Thread: Unable to install some packages in R

  1. #11

    Default Re: Unable to install some packages in R

    Quote Originally Posted by LiBurner1 View Post
    Ok. Thank you. I installed gcc-fortran and after many many warning during the installation process it works.
    I have got the VGAM package. But this is not the solution to all my problems.

    The next package is called lme4 and I get the following:

    Code:
    install.packages("lme4")
    Installing package into ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5’
    (as ‘lib’ is unspecified)
    also installing the dependency ‘nloptr’
    
    trying URL 'https://cran.rstudio.com/src/contrib/nloptr_1.2.1.tar.gz'
    Content type 'application/x-gzip' length 2448313 bytes (2.3 MB)
    ==================================================
    downloaded 2.3 MB
    
    trying URL 'https://cran.rstudio.com/src/contrib/lme4_1.1-21.tar.gz'
    Content type 'application/x-gzip' length 4124154 bytes (3.9 MB)
    ==================================================
    downloaded 3.9 MB
    
    * installing *source* package ‘nloptr’ ...
    ** package ‘nloptr’ successfully unpacked and MD5 sums checked
    configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
    checking whether the C++ compiler works... no
    configure: error: in `/tmp/RtmpD8kgd9/R.INSTALL30296e4b9c4d/nloptr':
    configure: error: C++ compiler cannot create executables
    See `config.log' for more details
    ERROR: configuration failed for package ‘nloptr’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/nloptr’
    Warning in install.packages :
      installation of package ‘nloptr’ had non-zero exit status
    ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/lme4’
    Warning in install.packages :
      installation of package ‘lme4’ had non-zero exit status
    
    The downloaded source packages are in
        ‘/tmp/Rtmpz1n5FC/downloaded_packages’
    I guess you can find the problem when I send the config.log file. Unfortunately, I cannot find one. Do you know how to open it or where it is?
    Or do we not need it and there is a faster way to proceed?

    Best

  2. #12
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    Default Re: Unable to install some packages in R

    Quote Originally Posted by LiBurner1 View Post
    I guess you can find the problem when I send the config.log file. Unfortunately, I cannot find one. Do you know how to open it or where it is?
    Or do we not need it and there is a faster way to proceed?

    Best
    Hi
    The output shows the error?

    Code:
    checking whether the C++ compiler works... no
    configure: error: in `/tmp/RtmpD8kgd9/R.INSTALL30296e4b9c4d/nloptr':
    configure: error: C++ compiler cannot create executables
    Install gcc-c++ package.
    Cheers Malcolm °¿° SUSE Knowledge Partner (Linux Counter #276890)
    SUSE SLE, openSUSE Leap/Tumbleweed (x86_64) | GNOME DE
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  3. #13

    Default Re: Unable to install some packages in R

    Ok. The output shows the error. That is true. But I don't always understand it. For the last case it was easy, but what shall I do here:
    I needed to shorten it a little bit:
    It starts where the problem starts:
    Code:
     install.packages("devtools")
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
    * DONE (processx)
    * installing *source* package ‘curl’ ...
    ** package ‘curl’ successfully unpacked and MD5 sums checked
    Package libcurl was not found in the pkg-config search path.
    Perhaps you should add the directory containing `libcurl.pc'
    to the PKG_CONFIG_PATH environment variable
    No package 'libcurl' found
    Package libcurl was not found in the pkg-config search path.
    Perhaps you should add the directory containing `libcurl.pc'
    to the PKG_CONFIG_PATH environment variable
    No package 'libcurl' found
    Using PKG_CFLAGS=
    Using PKG_LIBS=-lcurl
    ------------------------- ANTICONF ERROR ---------------------------
    Configuration failed because libcurl was not found. Try installing:
     * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
     * rpm: libcurl-devel (Fedora, CentOS, RHEL)
     * csw: libcurl_dev (Solaris)
    If libcurl is already installed, check that 'pkg-config' is in your
    PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
    is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
    R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
    --------------------------------------------------------------------
    ERROR: configuration failed for package ‘curl’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/curl’
    Warning in install.packages :
      installation of package ‘curl’ had non-zero exit status
    
    ...
    
    
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    Error : /tmp/Rtmpo9bkE1/R.INSTALL1fff7730ab1a/xml2/man/read_xml.Rd:48: unable to load shared object '/home/main/R/x86_64-suse-linux-gnu-library/3.5/xml2/libs/xml2.so':
      libicui18n.so.58: cannot open shared object file: No such file or directory
    ERROR: installing Rd objects failed for package ‘xml2’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/xml2’
    Warning in install.packages :
      installation of package ‘xml2’ had non-zero exit status
    * installing *source* package ‘evaluate’ ...
    ** package ‘evaluate’ successfully unpacked and MD5 sums checked
    ** R
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
    * DONE (evaluate)
    * installing *source* package ‘git2r’ ...
    ** package ‘git2r’ successfully unpacked and MD5 sums checked
    configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
    checking build system type... x86_64-unknown-linux-gnu
    checking host system type... x86_64-unknown-linux-gnu
    checking for gcc... gcc
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables... 
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking for pkg-config... /usr/bin/pkg-config
    checking pkg-config is at least version 0.9.0... yes
    configure: Package dependency requirement 'libgit2 >= 0.26.0' could not be satisfied.
    
      -----------------------------------------------------------------------
    
       Unable to find the libgit2 library on this system. Building 'git2r'
       using the bundled source of the libgit2 library.
    
       To build git2r with a system installation of libgit2, please install:
         libgit2-dev   (package on e.g. Debian and Ubuntu)
         libgit2-devel (package on e.g. Fedora, CentOS and RHEL)
         libgit2       (Homebrew package on OS X)
       and try again.
    
       If the libgit2 library is installed on your system but the git2r
       configuration is unable to find it, you can specify the include and
       lib path to libgit2 with:
    
       given you downloaded a tar-gz archive:
       R CMD INSTALL git2r-.tar.gz --configure-vars='INCLUDE_DIR=/path/to/include LIB_DIR=/path/to/lib'
    
       or cloned the GitHub git2r repository into a directory:
       R CMD INSTALL git2r/ --configure-vars='INCLUDE_DIR=/path/to/include LIB_DIR=/path/to/lib'
    
       or download and install git2r in R using
       install.packages('git2r', type='source', configure.vars='LIB_DIR=-L/path/to/libs INCLUDE_DIR=-I/path/to/headers')
    
       On macOS, another possibility is to let the configuration
       automatically download the libgit2 library from the Homebrew
       package manager with:
    
       R CMD INSTALL git2r-.tar.gz --configure-vars='autobrew=yes'
       or
       R CMD INSTALL git2r/ --configure-vars='autobrew=yes'
       or
       install.packages('git2r', type='source', configure.vars='autobrew=yes')
    
      -----------------------------------------------------------------------
    
    
    configure: Attempting configuration of bundled libgit2
    checking size of void*... 8
    checking for library containing inflate... no
    checking for zlib... no
    configure: error: in `/tmp/RtmpCQbEU1/R.INSTALL210e166e5106/git2r':
    configure: error: 
      ---------------------------------------------
       The zlib library that is required to build
       git2r was not found.
    
       Please install:
         zlib1g-dev (package on e.g. Debian and Ubuntu)
         zlib-devel (package on e.g. Fedora, CentOS and RHEL)
       and try again.
    
       If the zlib library is installed on your
       system but the git2r configuration is
       unable to find it, you can specify the
       include and lib path to zlib with:
       R CMD INSTALL git2r --configure-vars='LIBS=-L/path/to/libs CPPFLAGS=-I/path/to/headers'
      ---------------------------------------------
    See `config.log' for more details
    ERROR: configuration failed for package ‘git2r’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/git2r’
    Warning in install.packages :
      installation of package ‘git2r’ had non-zero exit status
    * installing *source* package ‘remotes’ ...
    ** package ‘remotes’ successfully unpacked and MD5 sums checked
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    * DONE (remotes)
    * installing *source* package ‘rprojroot’ ...
    ** package ‘rprojroot’ successfully unpacked and MD5 sums checked
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    * DONE (rprojroot)
    * installing *source* package ‘callr’ ...
    ** package ‘callr’ successfully unpacked and MD5 sums checked
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    * DONE (callr)
    ERROR: dependency ‘curl’ is not available for package ‘httr’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/httr’
    Warning in install.packages :
      installation of package ‘httr’ had non-zero exit status
    ERROR: dependency ‘xml2’ is not available for package ‘roxygen2’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/roxygen2’
    Warning in install.packages :
      installation of package ‘roxygen2’ had non-zero exit status
    
    ...
    
    installing to /home/main/R/x86_64-suse-linux-gnu-library/3.5/testthat/libs
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    *** copying figures
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    * DONE (testthat)
    ERROR: dependency ‘httr’ is not available for package ‘gh’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/gh’
    Warning in install.packages :
      installation of package ‘gh’ had non-zero exit status
    * installing *source* package ‘pkgbuild’ ...
    ** package ‘pkgbuild’ successfully unpacked and MD5 sums checked
    ** R
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
    * DONE (pkgbuild)
    ERROR: dependencies ‘curl’, ‘gh’, ‘git2r’ are not available for package ‘usethis’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/usethis’
    Warning in install.packages :
      installation of package ‘usethis’ had non-zero exit status
    * installing *source* package ‘rcmdcheck’ ...
    ** package ‘rcmdcheck’ successfully unpacked and MD5 sums checked
    ** R
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded
    * DONE (rcmdcheck)
    ERROR: dependencies ‘usethis’, ‘git2r’, ‘httr’, ‘roxygen2’ are not available for package ‘devtools’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/devtools’
    Warning in install.packages :
      installation of package ‘devtools’ had non-zero exit status
    
    The downloaded source packages are in
        ‘/tmp/RtmpJV1uKW/downloaded_packages’
    Best

  4. #14
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    Default Re: Unable to install some packages in R

    Hi
    Just search for the base name given and look for the development package, eg curl is libcurl-devel, git, libgit2-devel etc
    Cheers Malcolm °¿° SUSE Knowledge Partner (Linux Counter #276890)
    SUSE SLE, openSUSE Leap/Tumbleweed (x86_64) | GNOME DE
    If you find this post helpful and are logged into the web interface,
    please show your appreciation and click on the star below... Thanks!

  5. #15

    Default Re: Unable to install some packages in R

    Quote Originally Posted by malcolmlewis View Post
    Hi
    Just search for the base name given and look for the development package, eg curl is libcurl-devel, git, libgit2-devel etc
    Ok. Installed those + two more. Now the problem narrows down to "gh":

    Code:
    > install.packages("devtools")
    
    ...
    
    * installing *source* package ‘gh’ ...
    ** package ‘gh’ successfully unpacked and MD5 sums checked
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in rbind(info, getNamespaceInfo(env, "S3methods")) : 
      number of columns of matrices must match (see arg 2)
    ERROR: lazy loading failed for package ‘gh’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/gh’
    Warning in install.packages :
      installation of package ‘gh’ had non-zero exit status
    
    ...
    
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    Error : /tmp/RtmpicGJCV/R.INSTALL1c8815f0fd60/xml2/man/read_xml.Rd:48: unable to load shared object '/home/main/R/x86_64-suse-linux-gnu-library/3.5/xml2/libs/xml2.so':
      libicui18n.so.58: cannot open shared object file: No such file or directory
    ERROR: installing Rd objects failed for package ‘xml2’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/xml2’
    Warning in install.packages :
      installation of package ‘xml2’ had non-zero exit status
    ERROR: dependency ‘gh’ is not available for package ‘usethis’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/usethis’
    Warning in install.packages :
      installation of package ‘usethis’ had non-zero exit status
    ERROR: dependency ‘xml2’ is not available for package ‘roxygen2’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/roxygen2’
    Warning in install.packages :
      installation of package ‘roxygen2’ had non-zero exit status
    ERROR: dependencies ‘usethis’, ‘roxygen2’ are not available for package ‘devtools’
    * removing ‘/home/main/R/x86_64-suse-linux-gnu-library/3.5/devtools’
    Warning in install.packages :
      installation of package ‘devtools’ had non-zero exit status
    
    The downloaded source packages are in
        ‘/tmp/RtmpTRVjrX/downloaded_packages’
    Error in dyn.load(file, DLLpath = DLLpath, ...) : 
      unable to load shared object '/usr/lib64/R/library/yaml/libs/yaml.so':
      /usr/lib64/R/library/yaml/libs/yaml.so: undefined symbol: MARK_NOT_MUTABLE
    Error in dyn.load(file, DLLpath = DLLpath, ...) : 
      unable to load shared object '/usr/lib64/R/library/yaml/libs/yaml.so':
      /usr/lib64/R/library/yaml/libs/yaml.so: undefined symbol: MARK_NOT_MUTABLE

  6. #16

    Default Re: Unable to install some packages in R

    I downloaded the gh package as zip and put the package into my R packages folder.
    But it still isn't working:
    Code:
    > library("gh", lib.loc="~/R/x86_64-suse-linux-gnu-library/3.5")
    Error: package or namespace load failed for ‘gh’ in rbind(info, getNamespaceInfo(env, "S3methods")):
     number of columns of matrices must match (see arg 2)
    In addition: Warning message:
    package ‘gh’ was built under R version 3.6.0
    It also doesn't work, when I download the older version.

    Any idea?

    Best

  7. #17
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    Default Re: Unable to install some packages in R

    Hi
    Have you tried removing the .RData and .Rhistory files from the package folder and building again?
    Cheers Malcolm °¿° SUSE Knowledge Partner (Linux Counter #276890)
    SUSE SLE, openSUSE Leap/Tumbleweed (x86_64) | GNOME DE
    If you find this post helpful and are logged into the web interface,
    please show your appreciation and click on the star below... Thanks!

  8. #18

    Default Re: Unable to install some packages in R

    Quote Originally Posted by malcolmlewis View Post
    Hi
    Have you tried removing the .RData and .Rhistory files from the package folder and building again?
    There are no such files. There are .RData files in another package. I deleted the whole package, but it did not change anything.

    Best

  9. #19
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    Default Re: Unable to install some packages in R

    The following describes your error in a different scenario... on Windows (debatable whether is relevant) and trying to install and run ggplot on an already installed R (who knows whether R was installed properly in the first place)

    https://community.rstudio.com/t/ggpl...error/32806/17

    In the above scenario, one of the commentators suggested there could be a major difference between R versions 3.5 and 3.6.
    Note also that your error says that the gh you're trying to install was built for 3.6 whereas you're trying to install 3.5.

    I would suggest removing what you have installed and just install 3.6, you will have to add the following repository using the following command
    Code:
    zypper ar -f http://download.opensuse.org/reposit...USE_Leap_15.1/ LEAP_15.1_R_repository
    HTH,
    TSU
    Beginner Wiki Quickstart - https://en.opensuse.org/User:Tsu2/Quickstart_Wiki
    Solved a problem recently? Create a wiki page for future personal reference!
    Learn something new?
    Attended a computing event?
    Post and Share!

  10. #20

    Default Re: Unable to install some packages in R

    Quote Originally Posted by tsu2 View Post
    The following describes your error in a different scenario... on Windows (debatable whether is relevant) and trying to install and run ggplot on an already installed R (who knows whether R was installed properly in the first place)

    https://community.rstudio.com/t/ggpl...error/32806/17

    In the above scenario, one of the commentators suggested there could be a major difference between R versions 3.5 and 3.6.
    Note also that your error says that the gh you're trying to install was built for 3.6 whereas you're trying to install 3.5.

    I would suggest removing what you have installed and just install 3.6, you will have to add the following repository using the following command
    Code:
    zypper ar -f http://download.opensuse.org/reposit...USE_Leap_15.1/ LEAP_15.1_R_repository
    HTH,
    TSU
    I would like to get 3.6. But there is only 3.5 available for Leap 15.1
    See: https://software.opensuse.org/package/R-base

    I don't think this was the main problem as I could also get the old release of the "gh"-package and it also did not work. The only thing that changes is that the "in addition" error is not there anymore.

    I downloaded your repository although don't understand for what it is for.
    But it also does not seem to work:
    [sudo] password for root:
    Retrieving repository 'LEAP_15.1_R_repository' metadata .................[error]
    Repository 'LEAP_15.1_R_repository' is invalid.
    [LEAP_15.1_R_repository|http://download.opensuse.org/reposit...USE_Leap_15.1/] Valid metadata not found at specified URL

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