BiocManager problem.

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

BiocManager problem.

Ali Siavosh
Hi,
I have installation of R in a server running on redhat 7. I have upgraded R and now to upgrade BiocManager I get error messages as below:

> install.packages("BiocManager")
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.revolutionanalytics.com/src/contrib/BiocManager_1.30.7.tar.gz'
Content type 'application/octet-stream' length 38020 bytes (37 KB)
==================================================
downloaded 37 KB

* installing *source* package ‘BiocManager’ ...
** package ‘BiocManager’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘BiocManager’
    finding HTML links ... done
    BiocManager-pkg                         html  
    available                               html  
    install                                 html  
    repositories                            html  
    valid                                   html  
    version                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocManager)
Making 'packages.html' ... done

The downloaded source packages are in
        ‘/tmp/RtmpgHhwMp/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
> BiocManager::version()
Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
  call: NULL
  error: Bioconductor version '3.8' requires R version '3.5'; see
  https://bioconductor.org/install
> BiocManager::valid()
Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
  call: NULL
  error: Bioconductor version '3.8' requires R version '3.5'; see
  https://bioconductor.org/install
> BiocManager::install(version="3.5")
Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
  call: NULL
  error: Bioconductor version '3.8' requires R version '3.5'; see
  https://bioconductor.org/install
> BiocManager::install(version="3.7")
Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
  call: NULL
  error: Bioconductor version '3.8' requires R version '3.5'; see
  https://bioconductor.org/install <https://bioconductor.org/install>


I appreciate any help with regard to this.
Thank you


        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: BiocManager problem.

Martin Morgan-4
Please follow the response to your question on the Bioconductor support site

https://support.bioconductor.org/p/125493/

Martin Morgan

On 10/10/19, 12:23 PM, "R-help on behalf of Ali Siavosh" <[hidden email] on behalf of [hidden email]> wrote:

    Hi,
    I have installation of R in a server running on redhat 7. I have upgraded R and now to upgrade BiocManager I get error messages as below:
   
    > install.packages("BiocManager")
    Installing package into ‘/usr/lib64/R/library’
    (as ‘lib’ is unspecified)
    trying URL 'https://cran.revolutionanalytics.com/src/contrib/BiocManager_1.30.7.tar.gz'
    Content type 'application/octet-stream' length 38020 bytes (37 KB)
    ==================================================
    downloaded 37 KB
   
    * installing *source* package ‘BiocManager’ ...
    ** package ‘BiocManager’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
      converting help for package ‘BiocManager’
        finding HTML links ... done
        BiocManager-pkg                         html  
        available                               html  
        install                                 html  
        repositories                            html  
        valid                                   html  
        version                                 html  
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
    * DONE (BiocManager)
    Making 'packages.html' ... done
   
    The downloaded source packages are in
    ‘/tmp/RtmpgHhwMp/downloaded_packages’
    Updating HTML index of packages in '.Library'
    Making 'packages.html' ... done
    > BiocManager::version()
    Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
      call: NULL
      error: Bioconductor version '3.8' requires R version '3.5'; see
      https://bioconductor.org/install
    > BiocManager::valid()
    Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
      call: NULL
      error: Bioconductor version '3.8' requires R version '3.5'; see
      https://bioconductor.org/install
    > BiocManager::install(version="3.5")
    Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
      call: NULL
      error: Bioconductor version '3.8' requires R version '3.5'; see
      https://bioconductor.org/install
    > BiocManager::install(version="3.7")
    Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
      call: NULL
      error: Bioconductor version '3.8' requires R version '3.5'; see
      https://bioconductor.org/install <https://bioconductor.org/install>
   
   
    I appreciate any help with regard to this.
    Thank you
   
   
    [[alternative HTML version deleted]]
   
    ______________________________________________
    [hidden email] mailing list -- To UNSUBSCRIBE and more, see
    https://stat.ethz.ch/mailman/listinfo/r-help
    PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    and provide commented, minimal, self-contained, reproducible code.
   
______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: BiocManager problem.

Ali Siavosh
All good.
Thanks

> On Oct 10, 2019, at 1:08 PM, Martin Morgan <[hidden email]> wrote:
>
> Please follow the response to your question on the Bioconductor support site
>
> https://support.bioconductor.org/p/125493/
>
> Martin Morgan
>
> On 10/10/19, 12:23 PM, "R-help on behalf of Ali Siavosh" <[hidden email] on behalf of [hidden email]> wrote:
>
>    Hi,
>    I have installation of R in a server running on redhat 7. I have upgraded R and now to upgrade BiocManager I get error messages as below:
>
>> install.packages("BiocManager")
>    Installing package into ‘/usr/lib64/R/library’
>    (as ‘lib’ is unspecified)
>    trying URL 'https://cran.revolutionanalytics.com/src/contrib/BiocManager_1.30.7.tar.gz'
>    Content type 'application/octet-stream' length 38020 bytes (37 KB)
>    ==================================================
>    downloaded 37 KB
>
>    * installing *source* package ‘BiocManager’ ...
>    ** package ‘BiocManager’ successfully unpacked and MD5 sums checked
>    ** using staged installation
>    ** R
>    ** inst
>    ** byte-compile and prepare package for lazy loading
>    ** help
>    *** installing help indices
>      converting help for package ‘BiocManager’
>        finding HTML links ... done
>        BiocManager-pkg                         html  
>        available                               html  
>        install                                 html  
>        repositories                            html  
>        valid                                   html  
>        version                                 html  
>    ** building package indices
>    ** installing vignettes
>    ** testing if installed package can be loaded from temporary location
>    ** testing if installed package can be loaded from final location
>    ** testing if installed package keeps a record of temporary installation path
>    * DONE (BiocManager)
>    Making 'packages.html' ... done
>
>    The downloaded source packages are in
>     ‘/tmp/RtmpgHhwMp/downloaded_packages’
>    Updating HTML index of packages in '.Library'
>    Making 'packages.html' ... done
>> BiocManager::version()
>    Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
>      call: NULL
>      error: Bioconductor version '3.8' requires R version '3.5'; see
>      https://bioconductor.org/install
>> BiocManager::valid()
>    Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
>      call: NULL
>      error: Bioconductor version '3.8' requires R version '3.5'; see
>      https://bioconductor.org/install
>> BiocManager::install(version="3.5")
>    Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
>      call: NULL
>      error: Bioconductor version '3.8' requires R version '3.5'; see
>      https://bioconductor.org/install
>> BiocManager::install(version="3.7")
>    Error: .onLoad failed in loadNamespace() for 'BiocManager', details:
>      call: NULL
>      error: Bioconductor version '3.8' requires R version '3.5'; see
>      https://bioconductor.org/install <https://bioconductor.org/install>
>
>
>    I appreciate any help with regard to this.
>    Thank you
>
>
>     [[alternative HTML version deleted]]
>
>    ______________________________________________
>    [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>    https://stat.ethz.ch/mailman/listinfo/r-help
>    PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>    and provide commented, minimal, self-contained, reproducible code.
>

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.