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Hello,
I am having troubles installing the synapter package, I get the error:
package ‘synapter’ is not available for Bioconductor version '3.14'
> sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocVersion_3.14.0 BiocManager_1.30.16
loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2
When I try to isntall synapter it appears the installer tries to use the system library instead of my personal one, which I currently use without any specification (e.g. isntall.packages() )
> if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
>
> BiocManager::install("synapter")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'synapter'
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.1.2/library packages:
class, foreign, MASS, Matrix, nlme, nnet, rpart, spatial
Warning message:
In .inet_warning(msg) :
package ‘synapter’ is not available for Bioconductor version '3.14'
A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
since it is not using the library I normally use, I set it up manually but it still doesn't work
> BiocManager::install(lib=.libPaths()[1])
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
> BiocManager::install("synapter",lib=.libPaths()[1])
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'synapter'
Warning message:
In .inet_warning(msg) :
package ‘synapter’ is not available for Bioconductor version '3.14'
A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> dim(available.packages("https://bioconductor.org/packages/3.14/bioc/src/contrib"))
[1] 2070 17
Any ideas on how to install the package?
Thanks for any help :) CZ
Also, please note that the message you are getting from
install.packageshas to do with the recommended packages that come with R, rather than the one you are trying to install. Generally speaking, R on Windows is installed in a privileged location that you as a normal user do not have write privileges. The recommended packages get installed in a library directory in that privileged location and if there are updates for them on CRAN,installwill try to update but fail. Which is why you get the warning about that. I personally don't bother updating the recommended packages, but you could do so by running R as an administrator and then usinginstall. But you should not run R as administrator in regular use.thanks! it worked :-)