Error: cannot remove prior installation of package ‘BiocManager’

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Error: cannot remove prior installation of package ‘BiocManager’

Ankush Sharma
Dear all,

I am working R version 4.0.1 macos catalina , I´m not able to load
libraries e.g ggplot2

Error: Error: package or namespace load failed for ‘ggplot2’ in
loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘gtable’
Then i tried installing gtable,  But  installation is showing error :
Error in install.packages : cannot remove prior installation of package
‘gtable’

This is also for other packages like BiocManager, when I manually changed
the name or removed the BiocManager from the library, the package was
smoothly installed.
Any pointers on how to solve this problem without manual removal of
packages.  remove.packages command is also not working.

Thanks in advance.

Best Regards
*Ankush Sharma*

        [[alternative HTML version deleted]]

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Re: Error: cannot remove prior installation of package ‘BiocManager’

Uwe Ligges-3
The packages must not be loaded when you try to update.

Best,
Uwe Ligges



On 19.06.2020 12:07, Ankush Sharma wrote:

> Dear all,
>
> I am working R version 4.0.1 macos catalina , I´m not able to load
> libraries e.g ggplot2
>
> Error: Error: package or namespace load failed for ‘ggplot2’ in
> loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
>   there is no package called ‘gtable’
> Then i tried installing gtable,  But  installation is showing error :
> Error in install.packages : cannot remove prior installation of package
> ‘gtable’
>
> This is also for other packages like BiocManager, when I manually changed
> the name or removed the BiocManager from the library, the package was
> smoothly installed.
> Any pointers on how to solve this problem without manual removal of
> packages.  remove.packages command is also not working.
>
> Thanks in advance.
>
> Best Regards
> *Ankush Sharma*
>
> [[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.
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Re: Error: cannot remove prior installation of package ‘BiocManager’

Ankush Sharma
The packages were installed after the update!

Best Regards
*Ankush Sharma*


On Fri, Jun 19, 2020 at 1:56 PM Uwe Ligges <[hidden email]>
wrote:

> The packages must not be loaded when you try to update.
>
> Best,
> Uwe Ligges
>
>
>
> On 19.06.2020 12:07, Ankush Sharma wrote:
> > Dear all,
> >
> > I am working R version 4.0.1 macos catalina , I´m not able to load
> > libraries e.g ggplot2
> >
> > Error: Error: package or namespace load failed for ‘ggplot2’ in
> > loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
> >   there is no package called ‘gtable’
> > Then i tried installing gtable,  But  installation is showing error :
> > Error in install.packages : cannot remove prior installation of package
> > ‘gtable’
> >
> > This is also for other packages like BiocManager, when I manually changed
> > the name or removed the BiocManager from the library, the package was
> > smoothly installed.
> > Any pointers on how to solve this problem without manual removal of
> > packages.  remove.packages command is also not working.
> >
> > Thanks in advance.
> >
> > Best Regards
> > *Ankush Sharma*
> >
> >       [[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.
> >
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Error: cannot remove prior installation of package ‘BiocManager’

Duncan Murdoch-2
On 19/06/2020 8:06 a.m., Ankush Sharma wrote:
> The packages were installed after the update!

That's not relevant.  The issue is that the packages were loaded at the
time you tried to update them.

You may have to start R with the --vanilla option to avoid automatically
loading packages if you've got a .Rprofile (or similar) file running
automatically on startup.

A simpler solution to this is to use RStudio; it will automatically
restart R if necessary when installing a package.

Duncan Murdoch

>
> Best Regards
> *Ankush Sharma*
>
>
> On Fri, Jun 19, 2020 at 1:56 PM Uwe Ligges <[hidden email]>
> wrote:
>
>> The packages must not be loaded when you try to update.
>>
>> Best,
>> Uwe Ligges
>>
>>
>>
>> On 19.06.2020 12:07, Ankush Sharma wrote:
>>> Dear all,
>>>
>>> I am working R version 4.0.1 macos catalina , I´m not able to load
>>> libraries e.g ggplot2
>>>
>>> Error: Error: package or namespace load failed for ‘ggplot2’ in
>>> loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
>>>    there is no package called ‘gtable’
>>> Then i tried installing gtable,  But  installation is showing error :
>>> Error in install.packages : cannot remove prior installation of package
>>> ‘gtable’
>>>
>>> This is also for other packages like BiocManager, when I manually changed
>>> the name or removed the BiocManager from the library, the package was
>>> smoothly installed.
>>> Any pointers on how to solve this problem without manual removal of
>>> packages.  remove.packages command is also not working.
>>>
>>> Thanks in advance.
>>>
>>> Best Regards
>>> *Ankush Sharma*
>>>
>>>        [[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.
>>>
>>
>
> [[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.
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Re: Error: cannot remove prior installation of package ‘BiocManager’

Ankush Sharma
Thanks, Duncan and Uwe,
I was using Rstudio.  This solved the problem

Best Regards
*Ankush Sharma*


On Fri, Jun 19, 2020 at 2:25 PM Duncan Murdoch <[hidden email]>
wrote:

> On 19/06/2020 8:06 a.m., Ankush Sharma wrote:
> > The packages were installed after the update!
>
> That's not relevant.  The issue is that the packages were loaded at the
> time you tried to update them.
>
> You may have to start R with the --vanilla option to avoid automatically
> loading packages if you've got a .Rprofile (or similar) file running
> automatically on startup.
>
> A simpler solution to this is to use RStudio; it will automatically
> restart R if necessary when installing a package.
>
> Duncan Murdoch
>
> >
> > Best Regards
> > *Ankush Sharma*
> >
> >
> > On Fri, Jun 19, 2020 at 1:56 PM Uwe Ligges <
> [hidden email]>
> > wrote:
> >
> >> The packages must not be loaded when you try to update.
> >>
> >> Best,
> >> Uwe Ligges
> >>
> >>
> >>
> >> On 19.06.2020 12:07, Ankush Sharma wrote:
> >>> Dear all,
> >>>
> >>> I am working R version 4.0.1 macos catalina , I´m not able to load
> >>> libraries e.g ggplot2
> >>>
> >>> Error: Error: package or namespace load failed for ‘ggplot2’ in
> >>> loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
> >>>    there is no package called ‘gtable’
> >>> Then i tried installing gtable,  But  installation is showing error :
> >>> Error in install.packages : cannot remove prior installation of package
> >>> ‘gtable’
> >>>
> >>> This is also for other packages like BiocManager, when I manually
> changed
> >>> the name or removed the BiocManager from the library, the package was
> >>> smoothly installed.
> >>> Any pointers on how to solve this problem without manual removal of
> >>> packages.  remove.packages command is also not working.
> >>>
> >>> Thanks in advance.
> >>>
> >>> Best Regards
> >>> *Ankush Sharma*
> >>>
> >>>        [[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.
> >>>
> >>
> >
> >       [[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.
> >
>
>

        [[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.