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]]
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"
<r-help-bounces at r-project.org on behalf of ali.siavosh at gmail.com>
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]]
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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.
All good. Thanks> On Oct 10, 2019, at 1:08 PM, Martin Morgan <mtmorgan.bioc at gmail.com> 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" <r-help-bounces at r-project.org on behalf of ali.siavosh at gmail.com> 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]] > > ______________________________________________ > R-help at r-project.org 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. >