[Bioc-devel] avoid updating BiocManager to 1.30.13; provisional fix available
A problem has been observed with the version of BiocManager
currently available at CRAN. Do not upgrade to 1.30.13.
If you have already done so, please use
devtools::install_github("Bioconductor/BiocManager", ref="ghost-binary-repo"
)
and restart R; this will provide BiocManager 1.30.13.1
If you run into problems with this please let me know.
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Re: [Bioc-devel] Can't install Bioconductor 3.13 under Windows 10
This is a known problem and is being investigated. Thanks for the report.
On Sat, May 8, 2021 at 8:18 AM Gordon K Smyth wrote:
> I am currently unable to install any Bioconductor 3.13 packages using
> BiocManager for Windows. Here is a sample R session using R 4.1.0beta for
> Windows. Notice the first time I type `install("Biobase")` there is no
> error message but the package is not installed. The second time and
> subsequent times I use install() I get an error message mentioning
> `readRDS`.
>
> Any ideas?
> Thanks
> Gordon
>
> > library(BiocManager)
> Bioconductor version 3.13 (BiocManager 1.30.13), ?BiocManager::install for
> help
> > install("Biobase")
> Bioconductor version 3.13 (BiocManager 1.30.13), R 4.1.0 beta (2021-05-06
> r80268)
> Installing package(s) 'BiocVersion', 'Biobase'
> also installing the dependency ‘BiocGenerics’
>
> > library(Biobase)
> Error in library(Biobase) : there is no package called ‘Biobase’
> > install("Biobase")
> Bioconductor version 3.13 (BiocManager 1.30.13), R 4.1.0 beta (2021-05-06
> r80268)
> Installing package(s) 'BiocVersion', 'Biobase'
> also installing the dependency ‘BiocGenerics’
>
> Error in readRDS(dest) : error reading from connection
> > sessionInfo()
> R version 4.1.0 beta (2021-05-06 r80268)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 18363)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
> [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocManager_1.30.13
>
> loaded via a namespace (and not attached):
> [1] compiler_4.1.0 tools_4.1.0
>
> --
> Professor Gordon K Smyth
> Joint Head, Bioinformatics Division
> Walter and Eliza Hall Institute of Medical Research
>
> [WEHI Logo]
>
>
> Walter and Eliza Hall Institute of Medical Research
> 1G Royal Parade Parkville Victoria 3052 Australia
>
> www.wehi.edu.au
>
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> https://www.facebook.com/WEHIresearch/> | Instagram<
> https://www.instagram.com/wehi_research> | Youtube<
> https://www.youtube.com/user/WEHImovies> | LinkedIn<
> https://www.linkedin.com/company/wehi_research>
>
>
> WEHI acknowledges the Wurundjeri people of the Kulin Nation as the
> traditional owners of the land where our campuses are located and the
> continuing connection to country and community.
>
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[Bioc-devel] Can't install Bioconductor 3.13 under Windows 10
I am currently unable to install any Bioconductor 3.13 packages using
BiocManager for Windows. Here is a sample R session using R 4.1.0beta for
Windows. Notice the first time I type `install("Biobase")` there is no error
message but the package is not installed. The second time and subsequent times
I use install() I get an error message mentioning `readRDS`.
Any ideas?
Thanks
Gordon
> library(BiocManager)
Bioconductor version 3.13 (BiocManager 1.30.13), ?BiocManager::install for help
> install("Biobase")
Bioconductor version 3.13 (BiocManager 1.30.13), R 4.1.0 beta (2021-05-06
r80268)
Installing package(s) 'BiocVersion', 'Biobase'
also installing the dependency ‘BiocGenerics’
> library(Biobase)
Error in library(Biobase) : there is no package called ‘Biobase’
> install("Biobase")
Bioconductor version 3.13 (BiocManager 1.30.13), R 4.1.0 beta (2021-05-06
r80268)
Installing package(s) 'BiocVersion', 'Biobase'
also installing the dependency ‘BiocGenerics’
Error in readRDS(dest) : error reading from connection
> sessionInfo()
R version 4.1.0 beta (2021-05-06 r80268)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.13
loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0
--
Professor Gordon K Smyth
Joint Head, Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
[WEHI Logo]
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade Parkville Victoria 3052 Australia
www.wehi.edu.au
Twitter |
Facebook |
Youtube |
LinkedIn
WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional
owners of the land where our campuses are located and the continuing connection
to country and community.
Private and confidential
The content of this e-mail and any attachments may be private and confidential,
intended only for use of the individual or entity named. If you are not the
intended recipient of this message you must not read, forward, print, copy,
disclose, use or store in any way the information this e-mail or any attachment
contains. If you are not the intended recipient, please notify the sender
immediately and delete or destroy all copies of this e-mail and any attachment.
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