[R-pkg-devel] rtracklayer installation problems

Hi everyone,

  

I hope this is the right e-mail I should have used; this is the first time
that I ask for help with R!

Yesterday, I installed the devel version of R (4.1) as I need to use a
package (RiboDiPa) which only works for this version.

The package requires, among the others, the package "rtracklayer". Since
yesterday I am struggling trying to install rtracklayer for devel version
without success.

Below you can find the final message I got before the installation stops.
Any idea of what might be the reason why I cannot install rtracklayer?

  

ucsc/udc.c:46:10: fatal error: sys/mman.h: No such file or directory

#include <sys/mman.h>

           ^~~~~~~~~~~~

compilation terminated.

make: *** [Makevars.win:16: ucsc/udc.o] Error 1

ERROR: compilation failed for package 'rtracklayer'

* removing 'C:/Users/Rosario/Documents/R/win-library/4.1/rtracklayer'

  

If you need any other information please, do not hesitate to ask.

Thank you in advance for your help!

rtracklayer is a Bioconductor package, so you're probably better off 
asking on their support site https://support.bioconductor.org/.  When 
you do, please show the command you used for the install; it's possible 
a simple change there will fix things.

Duncan Murdoch

Hi, Rosario,

The message is telling you that you need to install the development header files for glibc on your computer.  This is a set of files that are needed for building some kinds of software, but are not installed by default.  Are you working on some sort of Linux machine?  On Centos 8, the relevant package to install is called "glibc-headers".  On Ubuntu 20.04 it's "libc6-dev".  You'd need to run a command in the shell, something like:

Centos:

sudo dnf install glibc-headers

or

sudo yum install glibc-headers

Ubuntu/Debian:

sudo apt install libc6-dev

If it's Windows or Mac, I can't help...

If you don't have root access on your host, or the above doesn't make sense to you, you will need to talk to whoever administers your computing environment, asking them to install the relevant package.

Hope this helps.

 - Gord


?On 20210407, 11:03, "R-package-devel on behalf of rosario.avolio at unina.it" <r-package-devel-bounces at r-project.org on behalf of rosario.avolio at unina.it> wrote:

    Hi everyone,



    I hope this is the right e-mail I should have used; this is the first time
    that I ask for help with R!

    Yesterday, I installed the devel version of R (4.1) as I need to use a
    package (RiboDiPa) which only works for this version.

    The package requires, among the others, the package "rtracklayer". Since
    yesterday I am struggling trying to install rtracklayer for devel version
    without success.

    Below you can find the final message I got before the installation stops.
    Any idea of what might be the reason why I cannot install rtracklayer? 



    ucsc/udc.c:46:10: fatal error: sys/mman.h: No such file or directory

    #include <sys/mman.h>

              ^~~~~~~~~~~~

    compilation terminated.

    make: *** [https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fMakevars.win%3a16&c=E,1,aB4mtmdcaXh3y_rFcDWiXKtEvYZoLA3GcTOtz2EAwNVyTaBV0cLYVfIMvPNYj-c9QK7LiaHqut3FcMfCLlVShgqSAdXj_xGXP8nS49zX7vVKE9rNPhmLmWDTnyU,&typo=1: ucsc/udc.o] Error 1

    ERROR: compilation failed for package 'rtracklayer'

    * removing 'C:/Users/Rosario/Documents/R/win-library/4.1/rtracklayer'



    If you need any other information please, do not hesitate to ask.

    Thank you in advance for your help!



    Best,

    Rosario





    Rosario Avolio, PhD

    Researcher

    Department of Molecular Medicine and Medical Biotechnology

    Via Pansini, 5

    19/A Building

    80131 Napoli, Italy

    email:  <mailto:rosario.avolio at unina.it> rosario.avolio at unina.it

    phone: +39 081 746 31 39





    ______________________________________________
    R-package-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-package-devel

(sorry, too quick on the return key)

?From the Bioconductor 'devel' (3.13, used with R-devel) 'landing page' for rtracklayer

https://bioconductor.org/packages/devel/rtracklayer

The 'build' badge is red; clicking on it shows a build system problem with rtracklayer on Windows. Scrolling on the landing page to the bottom shows

Source Package	rtracklayer_1.51.5.tar.gz
Windows Binary	
macOS 10.13 (High Sierra)	rtracklayer_1.51.5.tgz

so there is currently no Windows binary available. This is in the hands of the rtracklayer maintainer; there is a very high likelihood that it will be fixed, so either be patient or ask the rtracklayer maintainer directly to address this by, e.g., opening an issue at https://github.com/lawremi/rtracklayer

Martin Morgan


?On 4/7/21, 6:32 AM, "R-package-devel on behalf of Gordon Brown" <r-package-devel-bounces at r-project.org on behalf of Gordon.Brown at cruk.cam.ac.uk> wrote:

    Hi, Rosario,

    The message is telling you that you need to install the development header files for glibc on your computer.  This is a set of files that are needed for building some kinds of software, but are not installed by default.  Are you working on some sort of Linux machine?  On Centos 8, the relevant package to install is called "glibc-headers".  On Ubuntu 20.04 it's "libc6-dev".  You'd need to run a command in the shell, something like:

    Centos:
    > sudo dnf install glibc-headers
    or
    > sudo yum install glibc-headers

    Ubuntu/Debian:
    > sudo apt install libc6-dev

    If it's Windows or Mac, I can't help...

    If you don't have root access on your host, or the above doesn't make sense to you, you will need to talk to whoever administers your computing environment, asking them to install the relevant package.

    Hope this helps.

     - Gord


    ?On 20210407, 11:03, "R-package-devel on behalf of rosario.avolio at unina.it" <r-package-devel-bounces at r-project.org on behalf of rosario.avolio at unina.it> wrote:

        Hi everyone,



        I hope this is the right e-mail I should have used; this is the first time
        that I ask for help with R!

        Yesterday, I installed the devel version of R (4.1) as I need to use a
        package (RiboDiPa) which only works for this version.

        The package requires, among the others, the package "rtracklayer". Since
        yesterday I am struggling trying to install rtracklayer for devel version
        without success.

        Below you can find the final message I got before the installation stops.
        Any idea of what might be the reason why I cannot install rtracklayer? 



        ucsc/udc.c:46:10: fatal error: sys/mman.h: No such file or directory

        #include <sys/mman.h>

                  ^~~~~~~~~~~~

        compilation terminated.

        make: *** [https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fMakevars.win%3a16&c=E,1,aB4mtmdcaXh3y_rFcDWiXKtEvYZoLA3GcTOtz2EAwNVyTaBV0cLYVfIMvPNYj-c9QK7LiaHqut3FcMfCLlVShgqSAdXj_xGXP8nS49zX7vVKE9rNPhmLmWDTnyU,&typo=1: ucsc/udc.o] Error 1

        ERROR: compilation failed for package 'rtracklayer'

        * removing 'C:/Users/Rosario/Documents/R/win-library/4.1/rtracklayer'



        If you need any other information please, do not hesitate to ask.

        Thank you in advance for your help!



        Best,

        Rosario





        Rosario Avolio, PhD

        Researcher

        Department of Molecular Medicine and Medical Biotechnology

        Via Pansini, 5

        19/A Building

        80131 Napoli, Italy

        email:  <mailto:rosario.avolio at unina.it> rosario.avolio at unina.it

        phone: +39 081 746 31 39





        ______________________________________________
        R-package-devel at r-project.org mailing list
        https://stat.ethz.ch/mailman/listinfo/r-package-devel

    ______________________________________________
    R-package-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-package-devel