[R-pkg-devel] rtracklayer installation problems

Gordon Brown Gordon@Brown @end|ng |rom cruk@c@m@@c@uk
Wed Apr 7 12:32:27 CEST 2021

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:

> sudo dnf install glibc-headers
> sudo yum install glibc-headers

> 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 using unina.it" <r-package-devel-bounces using r-project.org on behalf of rosario.avolio using 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!



    Rosario Avolio, PhD


    Department of Molecular Medicine and Medical Biotechnology

    Via Pansini, 5

    19/A Building

    80131 Napoli, Italy

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

    phone: +39 081 746 31 39

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